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Sample records for proton nmr coupling

  1. Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2014-09-01

    Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min. PMID:25158224

  2. Proton zero-quantum 2D NMR of 2-propenenitrile aligned by an electric field. Determination of the 2H and 14N quadrupole coupling constants

    NASA Astrophysics Data System (ADS)

    Ruessink, B. H.; De Kanter, F. J. J.; MaClean, C.

    Zero-quantum NMR, selectively detected by 2D NMR, is applied to observe small 1H- 1H dipolar couplings in a polar liquid partially oriented by a strong electric field. The normal (single-quantum) 1H spectrum is severely broadened, which prevents the observation of small couplings. The results from the zero-quantum proton spectrum are used to calculate the 2H and 14N quadrupole coupling constants of 2-deutero-2-propenenitrile from the 2H and 14N NMR spectra.

  3. Minimalist Relativistic Force Field: Prediction of Proton-Proton Coupling Constants in (1)H NMR Spectra Is Perfected with NBO Hybridization Parameters.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2015-05-15

    We previously developed a reliable method for multiparametric scaling of Fermi contacts to achieve fast and accurate prediction of proton-proton spin-spin coupling constants (SSCC) in (1)H NMR. We now report that utilization of NBO hybridization coefficients for carbon atoms in the involved C-H bonds allows for a significant simplification of this parametric scheme, requiring only four general types of SSCCs: geminal, vicinal, 1,3-, and long-range constants. The method is optimized for inexpensive B3LYP/6-31G(d) molecular geometries. A new DU8 basis set, based on a training set of 475 experimental spin-spin coupling constants, is developed for hydrogen and common non-hydrogen atoms (Li, B, C, N, O, F, Si, P, S, Cl, Se, Br, I) to calculate Fermi contacts. On a test set of 919 SSCCs from a diverse collection of natural products and complex synthetic molecules the method gave excellent accuracy of 0.29 Hz (rmsd) with the maximum unsigned error not exceeding 1 Hz. PMID:25885091

  4. Carbon-proton scalar couplings in RNA. 3D heteronuclear and 2D isotope-edited NMR of a [sup 13]C-labeled extra-stable hairpin

    SciTech Connect

    Hines, J.V.; Landry, S.M.; Varani, G.; Tinoco, I. Jr. Lawrence Berkeley Lab., CA )

    1994-06-29

    Long range carbon-proton scalar couplings were measured for an RNA hairpin of 12 nucleotides using 3D and [sup 13]C-edited 2D NMR. The large one-bond carbon-proton scalar couplings ([sup 1]J[sub CH]) and small n-bond couplings ([sup 1]J[sub CH]) produce ECOSY type cross-peaks, thus facilitating the determination of the sign and magnitude of the smaller [sup 2]J[sub CH] or [sup 3]J[sub CH]. The UUCGRNA hairpin (5[prime]-rGGACUUCGGUCC-3[prime]), whose structure has been determined by our laboratory, was uniformly [sup 13]C-labeled at 30% isotopic enrichment. The observed [sup 1]J[sub CH] couplings were then correlated to the known structure. The signs of [sup 2]J[sub C4[prime]H5[prime

  5. Biochemical and proton NMR characterization of the isolated functional beta-subunit of coupling factor one from spinach chloroplasts

    SciTech Connect

    Roux-Fromy, M.; Neumann, J.M.; Andre, F.; Berger, G.; Girault, G.; Galmiche, J.M.; Remy, R.

    1987-04-29

    Beta subunits have been dissociated from CF1 of spinach chloroplasts, purified by HPLC and characterized by two-dimensional electrophoresis and fluorescence emission. The solutions of isolated beta subunits are able to hydrolyze MgATP; this ATPase activity is an intrinsic property of the beta molecule. From proton NMR at 300 and 500 MHz, it is shown that the preparations are fully reproducible and that beta subunits remain monomeric with 75% aliphatic protons associated with rigid parts of the molecule. The other 25% give rise to separate resonances and belong to mobile side-chains and/or to flexible regions. The measurement of the transverse relaxation times T2 has permitted a detailed characterization of the molecular dynamics of the isolated beta subunits.

  6. Proton-detected scalar coupling based assignment strategies in MAS solid-state NMR spectroscopy applied to perdeuterated proteins

    NASA Astrophysics Data System (ADS)

    Linser, Rasmus; Fink, Uwe; Reif, Bernd

    2008-07-01

    Assignment of proteins in MAS (magic angle spinning) solid-state NMR relies so far on correlations among heteronuclei. This strategy is based on well dispersed resonances in the 15N dimension. In many complex cases like membrane proteins or amyloid fibrils, an additional frequency dimension is desirable in order to spread the amide resonances. We show here that proton detected HNCO, HNCA, and HNCACB type experiments can successfully be implemented in the solid-state. Coherences are sufficiently long lived to allow pulse schemes of a duration greater than 70 ms before incrementation of the first indirect dimension. The achieved resolution is comparable to the resolution obtained in solution-state NMR experiments. We demonstrate the experiments using a triply labeled sample of the SH3 domain of chicken α-spectrin, which was re-crystallized in H 2O/D 2O using a ratio of 1/9. We employ paramagnetic relaxation enhancement (PRE) using EDTA chelated Cu II to enable rapid data acquisition.

  7. Sterically Demanding Multidentate Ligand Tris[(2-(6-methylpyridyl))methyl]amine Slows Exchange and Enhances Solution State Ligand Proton NMR Coupling to 199Hg(II)

    PubMed Central

    Bebout, Deborah C.; Bush, James F.; Crahan, Kathleen K.; Bowers, Edith V.; Butcher, Raymond J.

    2006-01-01

    The solution state coordination chemistry of Hg(ClO4)2 with tris[(2-(6-methylpyridyl))methyl]amine (TLA) was investigated in acetonitrile-d3 by proton NMR. Although Hg(II) is a d10 metal ion commonly associated with notoriously rapid exchange between coordination environments, as many as six ligand environments were observed to be in slow exchange on the chemical shift time scale at select metal-to-ligand ratios. One of these ligand environments was associated with extensive heteronuclear coupling between protons and 199Hg and was assigned to the complex [Hg(TLA)]2+. The 5J(1H199Hg) = 8 Hz associated with this complex is the first example of five-bond coupling in a nitrogen coordination compound of Hg(II). The spectral complexity of related studies conducted in acetone-d6 precluded analysis of coordination equilibria. Crystallographic characterization of the T-shaped complex [Hg(TLAH)(CH2COCH3)](ClO4)2 (1) in which two pyridyl rings are pendant suggested that the acidity of acetone combined with the poor coordinating abilities of the neutral solvent adds additional complexity to solution equilibria. The complex crystallizes in the triclinic space group P1¯ with a = 9.352(2) Å, b = 12.956(2) Å, c = 14.199(2) Å, α = 115.458(10)°, β = 90.286(11)°, γ = 108.445(11)°, and Z = 2. The HgNamine, Hg-Npyridyl, and Hg-C bond lengths in the complex are 2.614(4), 2.159(4), and 2.080(6) Å, respectively. Relevance to development of 199Hg NMR as a metallobioprobe is discussed. PMID:11978122

  8. Stretched poly(methyl methacrylate) gel aligns small organic molecules in chloroform. stereochemical analysis and diastereotopic proton NMR assignment in ludartin using residual dipolar couplings and 3J coupling constant analysis.

    PubMed

    Gil, Roberto R; Gayathri, Chakicherla; Tsarevsky, Nicolay V; Matyjaszewski, Krzysztof

    2008-02-01

    Poly(methyl methacrylate) (PMMA) gels prepared by copolymerizing methyl methacrylate (MMA) and various amounts of ethylene glycol dimethacrylate (EGDMA) in the presence of the radical initiator V-70 (2,2'-azobis(2,4-dimethyl-4-methoxyvaleronitrile)) can orient small organic molecules when swollen in NMR tubes with CDCl(3). The aligning properties of the stretched PMMA gels were evaluated by monitoring the quadrupolar splitting of the (2)H NMR signal of CDCl(3), and the aligning degree is proportional to the cross-linking density. Natural abundance one-bond (1)H-(13)C residual dipolar couplings (RDCs) for menthol measured in the gels depended on the cross-link density. The stereochemistry and assignment of the diastereotopic protons of the gastroprotective and nonsteroidal aromatase inhibitor sesquiterpene lactone ludartin, isolated from Stevia yaconensis var. subeglandulosa, were unambiguously determined using a combination of natural abundance one-bond (1)H-(13)C RDCs measured in a PMMA gel and a (3)J coupling constant analysis. PMID:18177050

  9. Resolution and measurement of heteronuclear dipolar couplings of a noncrystalline protein immobilized in a biological supramolecular assembly by proton-detected MAS solid-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Park, Sang Ho; Yang, Chen; Opella, Stanley J.; Mueller, Leonard J.

    2013-12-01

    Two-dimensional 15N chemical shift/1H chemical shift and three-dimensional 1H-15N dipolar coupling/15N chemical shift/1H chemical shift MAS solid-state NMR correlation spectra of the filamentous bacteriophage Pf1 major coat protein show single-site resolution in noncrystalline, intact-phage preparations. The high sensitivity and resolution result from 1H detection at 600 MHz under 50 kHz magic angle spinning using ∼0.5 mg of perdeuterated and uniformly 15N-labeled protein in which the exchangeable amide sites are partially or completely back-exchanged (reprotonated). Notably, the heteronuclear 1H-15N dipolar coupling frequency dimension is shown to select among 15N resonances, which will be useful in structural studies of larger proteins where the resonances exhibit a high degree of overlap in multidimensional chemical shift correlation spectra.

  10. Proton-Coupled Electron Transfer

    SciTech Connect

    Weinberg, Dave; Gagliardi, Christopher J.; Hull, Jonathan F; Murphy, Christine Fecenko; Kent, Caleb A.; Westlake, Brittany C.; Paul, Amit; Ess, Daniel H; McCafferty, Dewey Granville; Meyer, Thomas J

    2012-07-11

    Proton-Coupled Electron Transfer (PCET) describes reactions in which there is a change in both electron and proton content between reactants and products. It originates from the influence of changes in electron content on acid-base properties and provides a molecular-level basis for energy transduction between proton transfer and electron transfer. Coupled electron-proton transfer or EPT is defined as an elementary step in which electrons and protons transfer from different orbitals on the donor to different orbitals on the acceptor. There is (usually) a clear distinction between EPT and H-atom transfer (HAT) or hydride transfer, in which the transferring electrons and proton come from the same bond. Hybrid mechanisms exist in which the elementary steps are different for the reaction partners. EPT pathways such as PhO•/PhOH exchange have much in common with HAT pathways in that electronic coupling is significant, comparable to the reorganization energy with H{sub DA} ~ λ. Multiple-Site Electron-Proton Transfer (MS-EPT) is an elementary step in which an electron-proton donor transfers electrons and protons to different acceptors, or an electron-proton acceptor accepts electrons and protons from different donors. It exploits the long-range nature of electron transfer while providing for the short-range nature of proton transfer. A variety of EPT pathways exist, creating a taxonomy based on what is transferred, e.g., 1e-/2H+ MS-EPT. PCET achieves “redox potential leveling” between sequential couples and the buildup of multiple redox equivalents, which is of importance in multielectron catalysis. There are many examples of PCET and pH-dependent redox behavior in metal complexes, in organic and biological molecules, in excited states, and on surfaces. Changes in pH can be used to induce electron transfer through films and over long distances in molecules. Changes in pH, induced by local electron transfer, create pH gradients and a driving

  11. Theoretical and experimental study of 15N NMR protonation shifts.

    PubMed

    Semenov, Valentin A; Samultsev, Dmitry O; Krivdin, Leonid B

    2015-06-01

    A combined theoretical and experimental study revealed that the nature of the upfield (shielding) protonation effect in 15N NMR originates in the change of the contribution of the sp(2)-hybridized nitrogen lone pair on protonation resulting in a marked shielding of nitrogen of about 100 ppm. On the contrary, for amine-type nitrogen, protonation of the nitrogen lone pair results in the deshielding protonation effect of about 25 ppm, so that the total deshielding protonation effect of about 10 ppm is due to the interplay of the contributions of adjacent natural bond orbitals. A versatile computational scheme for the calculation of 15N NMR chemical shifts of protonated nitrogen species and their neutral precursors is proposed at the density functional theory level taking into account solvent effects within the supermolecule solvation model. PMID:25891386

  12. Cation Hydration Constants by Proton NMR: A Physical Chemistry Experiment.

    ERIC Educational Resources Information Center

    Smith, Robert L.; And Others

    1988-01-01

    Studies the polarization effect on water by cations and anions. Describes an experiment to illustrate the polarization effect of sodium, lithium, calcium, and strontium ions on the water molecule in the hydration spheres of the ions. Analysis is performed by proton NMR. (MVL)

  13. Synthesis and Proton NMR Spectroscopy of Intra-Vesicular Gamma-Aminobutyric Acid (GABA)*

    PubMed Central

    Wang, Luke Y.-J.; Tong, Rong; Kohane, Daniel S.

    2014-01-01

    We report the synthesis of vesicles containing gamma-aminobutyric acid (GABA), and their proton nuclear magnetic resonance (1H NMR) spectra. These vesicles were constructed to more closely mimic the intracellular environment wherein GABA exists. For this study, these GABA-containing vesicles were examined under 1H NMR as a potential platform for future studies on the differences between aqueous phantoms, ex vivo brain extracts, and in vivo magnetic resonance spectroscopy results. We found that intra-vesicular GABA faithfully yielded the chemical shifts and J-coupling constants of free aqueous GABA, alongside the chemical shift signals of the vesicle wall. PMID:24109882

  14. NMR Observation of Mobile Protons in Proton-Implanted ZnO Nanorods

    NASA Astrophysics Data System (ADS)

    Park, Jun Kue; Kwon, Hyeok-Jung; Lee, Cheol Eui

    2016-03-01

    The diffusion properties of H+ in ZnO nanorods are investigated before and after 20 MeV proton beam irradiation by using 1H nuclear magnetic resonance (NMR) spectroscopy. Herein, we unambiguously observe that the implanted protons occupy thermally unstable site of ZnO, giving rise to a narrow NMR line at 4.1 ppm. The activation barrier of the implanted protons was found to be 0.46 eV by means of the rotating-frame spin-lattice relaxation measurements, apparently being interstitial hydrogens. High-energy beam irradiation also leads to correlated jump diffusion of the surface hydroxyl group of multiple lines at ~1 ppm, implying the presence of structural disorder at the ZnO surface.

  15. NMR Observation of Mobile Protons in Proton-Implanted ZnO Nanorods

    PubMed Central

    Park, Jun Kue; Kwon, Hyeok-Jung; Lee, Cheol Eui

    2016-01-01

    The diffusion properties of H+ in ZnO nanorods are investigated before and after 20 MeV proton beam irradiation by using 1H nuclear magnetic resonance (NMR) spectroscopy. Herein, we unambiguously observe that the implanted protons occupy thermally unstable site of ZnO, giving rise to a narrow NMR line at 4.1 ppm. The activation barrier of the implanted protons was found to be 0.46 eV by means of the rotating-frame spin-lattice relaxation measurements, apparently being interstitial hydrogens. High-energy beam irradiation also leads to correlated jump diffusion of the surface hydroxyl group of multiple lines at ~1 ppm, implying the presence of structural disorder at the ZnO surface. PMID:26988733

  16. Proton conductors by the NMR method with modulation

    SciTech Connect

    Erofeev, L.N.; Sosikov, A.I.; Shteinberg, V.G.

    1988-01-01

    The NMR spectra and NMR relaxation in hydrates of phosphoro tungstic acid (PTA) and its salt were investigated. There was a narrow central line in both spectra, and the linewidth, measured in the temperature interval 130-290 K, was 4kHz. A previously proposed modulation technique by L. N. Erofeev, A.I. Sosikow, and A. K. Khitrin, was used to clarify the nature of the observed spectra. It was confirmed that model samples (gypsum, adamantane, rubber) make it possible to use the modulation technique to study the structure of proton systems. Decay curves for the magnetization in samples of PTA and Na-PTA are presented as obtained under multi-pulse spin locking conditions with and without modulation.

  17. Proton NMR studies of functionalized nanoparticles in aqueous environments

    NASA Astrophysics Data System (ADS)

    Tataurova, Yulia Nikolaevna

    in high-resolution NMR spectra. This technique is selective for protons on the surface organic functional groups due to their motional averaging in solution. In this study, 1H solution NMR spectroscopy was used to investigate the interface of the organic functional groups in D2O. The pKa for these functional groups covalently bound to the surface of nanoparticles was determined using an NMR-pH titration method based on the variation in the proton chemical shift for the alkyl group protons closest to the amine group with pH. The adsorption of toxic contaminants (chromate and arsenate anions) on the surface of functionalized silicalite-1 and mesoporous silica nanoparticles has been studied by 1H solution NMR spectroscopy. With this method, the surface bound contaminants are detected. The analysis of the intensity and position of these peaks allows quantitative assessment of the relative amounts of functional groups with adsorbed metal ions. These results demonstrate the sensitivity of solution NMR spectroscopy to the electronic environment and structure of the surface functional groups on porous nanomaterials.

  18. Heteronuclear NMR of DNA with the heteronucleus in natural abundance: facilitated assignment and extraction of coupling constants.

    PubMed Central

    Schmieder, P; Ippel, J H; van den Elst, H; van der Marel, G A; van Boom, J H; Altona, C; Kessler, H

    1992-01-01

    Two heteronuclear proton-carbon NMR experiments are applied to the DNA-octamer d(TTGGCCAA)2 with carbon in natural abundance. They lead to a complete assignment of the carbon resonances of the sugars and bases. In addition, several heteronuclear coupling constants, proton-carbon as well as proton-phosphorous and phosphorous-carbon, were determined. The information can be obtained in a reasonable measuring time and offers valuable information for a detailed picture of DNA structure. PMID:1408787

  19. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving.

    PubMed

    Pauli, Guido F; Niemitz, Matthias; Bisson, Jonathan; Lodewyk, Michael W; Soldi, Cristian; Shaw, Jared T; Tantillo, Dean J; Saya, Jordy M; Vos, Klaas; Kleinnijenhuis, Roel A; Hiemstra, Henk; Chen, Shao-Nong; McAlpine, James B; Lankin, David C; Friesen, J Brent

    2016-02-01

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of "structural correctness" depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D (1)H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D (1)H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by (1)H iterative full spin analysis (HiFSA). Fully characterized 1D (1)H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication. PMID:26812443

  20. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving

    PubMed Central

    2016-01-01

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of “structural correctness” depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D 1H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D 1H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by 1H iterative full spin analysis (HiFSA). Fully characterized 1D 1H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication. PMID:26812443

  1. HyperBIRD: a sensitivity-enhanced approach to collecting homonuclear-decoupled proton NMR spectra.

    PubMed

    Donovan, Kevin J; Frydman, Lucio

    2015-01-01

    Samples prepared following dissolution dynamic nuclear polarization (DNP) enable the detection of NMR spectra from low-γ nuclei with outstanding sensitivity, yet have limited use for the enhancement of abundant species like (1)H nuclei. Small- and intermediate-sized molecules, however, show strong heteronuclear cross-relaxation effects: spontaneous processes with an inherent isotopic selectivity, whereby only the (13)C-bonded protons receive a polarization enhancement. These effects are here combined with a recently developed method that delivers homonuclear-decoupled (1)H spectra in natural abundance samples based on heteronuclear couplings to these same, (13)C-bonded nuclei. This results in the HyperBIRD methodology; a single-shot combination of these two effects that can simultaneously simplify and resolve complex, congested (1)H NMR spectra with many overlapping spin multiplets, while achieving 50-100 times sensitivity enhancements over conventional thermal counterparts. PMID:25256418

  2. Intermediate couplings: NMR at the solids-liquids interface

    NASA Astrophysics Data System (ADS)

    Spence, Megan

    2006-03-01

    Anisotropic interactions like dipolar couplings and chemical shift anisotropy have long offered solid-state NMR spectroscopists valuable structural information. Recently, solution-state NMR structural studies have begun to exploit residual dipolar couplings of biological molecules in weakly anisotropic solutions. These residual couplings are about 0.1% of the coupling magnitudes observed in the solid state, allowing simple, high-resolution NMR spectra to be retained. In this work, we examine the membrane-associated opioid, leucine enkephalin (lenk), in which the ordering is ten times larger than that for residual dipolar coupling experiments, requiring a combination of solution-state and solid-state NMR techniques. We adapted conventional solid-state NMR techniques like adiabatic cross- polarization and REDOR for use with such a system, and measured small amide bond dipolar couplings in order to determine the orientation of the amide bonds (and therefore the peptide) with respect to the membrane surface. However, the couplings measured indicate large structural rearrangements on the surface and contradict the published structures obtained by NOESY constraints, a reminder that such methods are of limited use in the presence of large-scale dynamics.

  3. Structure of fully protonated proteins by proton-detected magic-angle spinning NMR.

    PubMed

    Andreas, Loren B; Jaudzems, Kristaps; Stanek, Jan; Lalli, Daniela; Bertarello, Andrea; Le Marchand, Tanguy; Cala-De Paepe, Diane; Kotelovica, Svetlana; Akopjana, Inara; Knott, Benno; Wegner, Sebastian; Engelke, Frank; Lesage, Anne; Emsley, Lyndon; Tars, Kaspars; Herrmann, Torsten; Pintacuda, Guido

    2016-08-16

    Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that, at 100-kHz MAS and above, spectral resolution is high enough to detect resolved correlations from amide and side-chain protons of all residue types, and to reliably measure a dense network of (1)H-(1)H proximities that define a protein structure. The high data quality allowed the correct identification of internuclear distance restraints encoded in 3D spectra with automated data analysis, resulting in accurate, unbiased, and fast structure determination. Additionally, we find that narrower proton resonance lines, longer coherence lifetimes, and improved magnetization transfer offset the reduced sample size at 100-kHz spinning and above. Less than 2 weeks of experiment time and a single 0.5-mg sample was sufficient for the acquisition of all data necessary for backbone and side-chain resonance assignment and unsupervised structure determination. We expect the technique to pave the way for atomic-resolution structure analysis applicable to a wide range of proteins. PMID:27489348

  4. Line-narrowing in proton-detected nitrogen-14 NMR

    NASA Astrophysics Data System (ADS)

    Cavadini, Simone; Vitzthum, Veronika; Ulzega, Simone; Abraham, Anuji; Bodenhausen, Geoffrey

    2010-01-01

    In solids spinning at the magic angle, the indirect detection of single-quantum (SQ) and double-quantum (DQ) 14N spectra ( I = 1) via spy nuclei S = 1/2 such as protons can be achieved in the manner of heteronuclear single- or multiple-quantum correlation (HSQC or HMQC) spectroscopy. The HMQC method relies on the excitation of two-spin coherences of the type T11IT11S and T21IT11S at the beginning of the evolution interval t1. The spectra obtained by Fourier transformation from t1 to ω1 may be broadened by the homogenous decay of the transverse terms of the spy nuclei S. This broadening is mostly due to homonuclear dipolar S- S' interactions between the proton spy nuclei. In this work we have investigated the possibility of inserting rotor-synchronized symmetry-based C or R sequences and decoupling schemes such as Phase-Modulated Lee-Goldburg (PMLG) sequences in the evolution period. These schemes reduce the homonuclear proton-proton interactions and lead to an enhancement of the resolution of both SQ and DQ proton-detected 14N HMQC spectra. In addition, we have investigated the combination of HSQC with symmetry-based sequences and PMLG and shown that the highest resolution in the 14N dimension is achieved by using HSQC in combination with symmetry-based sequences of the R-type. We show improvements in resolution in samples of L-alanine and the tripeptide ala-ala-gly (AAG). In particular, for L-alanine the width of the 14N SQ peak is reduced from 2 to 1.2 kHz, in agreement with simulations. We report accurate measurements of quadrupolar coupling constants and asymmetry parameters for amide 14N in AAG peptide bonds.

  5. NMR Spectra Transformed by Electron-Nuclear Coupling as Indicator of Structural Peculiarities of Magnetically Active Molecular Systems.

    PubMed

    Voronov, Vladimir K

    2016-09-01

    The peculiarities of nuclear spin relaxation in the paramagnetic systems have been analyzed taking into account the exchange processes. The analysis is based on the modified Solomon-Bloembergen equations. In this line, the conditions of detecting of the NMR signals of samples are discussed depending on resonance frequency of the NMR spectrometer and characteristic relaxation time. On this basis, (1)H NMR spectra of cobalt semiquinolate complex have been analyzed. It has been shown that the satellite signals observed in the spectrum are caused by hyperfine coupling of the tert-butyl group protons with α and β states (localized on pz orbital of the aromatic carbon) of unpaired electron spin. The relaxation process of the resonance protons is controlled by paramagnetic dipole-dipole coupling. The contact hyperfine coupling does not contribute to the paramagnetic broadening. A mechanism involving paramagnetic molecular structures, which are responsible for intramolecular exchange processes in the cobalt semiquinolate complex, is given. PMID:27513208

  6. Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

    SciTech Connect

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy

    2015-10-14

    Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), {sup 1}H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong {sup 1}H–{sup 1}H homonuclear dipolar couplings and narrow {sup 1}H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) {sup 1}H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about {sup 1}H–{sup 1}H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic

  7. Water Proton NMR for In Situ Detection of Insulin Aggregates.

    PubMed

    Taraban, Marc B; Truong, Huy C; Feng, Yue; Jouravleva, Elena V; Anisimov, Mikhail A; Yu, Yihua Bruce

    2015-12-01

    The need for quality control during the manufacturing and distribution of biopharmaceuticals is becoming increasingly necessary. At present, detecting drug degradation through the monitoring of active factor aggregation is accomplished through "invasive" techniques, such as size-exclusion chromatography (SEC), analytical ultracentrifugation (AUC), and so on. Unfortunately, these analytical methods require sampling the drug by opening the drug container that renders the remaining drug unusable regardless of the outcome of the test. Visual inspection, the current non-invasive quality control method is qualitative and can only detect visible particulates. Thus, it will miss sub-visible protein aggregates. In this paper, human insulin preparations were used to demonstrate that the transverse relaxation rate of water protons R2 ((1) H2 O) can serve as a sensitive and reliable indicator to detect and quantify both visible and sub-visible protein aggregates. R2 ((1) H2 O) is measured using a wide-bore low-field bench-top NMR instrument with permanent magnets. Such analysis could be carried out without opening the drug container, thus saving a drug for further use. The results suggest a novel, economical, non-destructive in situ analytical technique that allows for on-the-site quantification of protein aggregation in biopharmaceutical products. PMID:26344698

  8. Improvements in localized proton NMR spectroscopy of human brain. Water suppression, short echo times, and 1 ml resolution

    NASA Astrophysics Data System (ADS)

    Frahm, J.; Michaelis, T.; Merboldt, K. D.; Bruhn, H.; Gyngell, M. L.; Hänicke, W.

    Considerable technical improvements are reported for localized proton NMR spectroscopy using stimulated echoes. When compared to previous results, proton NMR spectra of the human brain are now obtainable (i) with in vivo water suppression factors of ⩾1000, (ii) with only minor T2 losses and negligible distortions due to J modulation at short echo times of 10-20 ms, and (iii) from volumes of interest as small as 1-8 ml within measuring times of 1-10 min. As a consequence, the detection of cerebral metabolites is greatly facilitated. This particularly applies to the assignment of those resonances (e.g., glutamate, taurine, inositols) that suffer from strong spin-spin coupling at the field strengths commonly in use for NMR in man. Studies of regional metabolite differences, tissue heterogeneity, and focal lesions in patients benefit from the increased spatial resolution and a concomitant reduction of partial volume effects. Localized proton NMR spectroscopy was performed on young healthy volunteers. Experiments were carried out on a 2.0 T whole-body MRI/MRS system using the standard headcoil for both imaging and spectroscopy.

  9. Configurationally-Coupled Protonation of Polyproline-7.

    PubMed

    Shi, Liuqing; Holliday, Alison E; Khanal, Neelam; Russell, David H; Clemmer, David E

    2015-07-15

    Structure and dynamics regulate protein function, but much less is known about how biomolecule-solvent interactions affect the structure-function relationship. Even less is known about the thermodynamics of biomolecule-solvent interactions and how such interactions influence conformational entropy. When transferred from propanol into 40:60 propanol:water under acidic conditions, a remarkably slow protonation reaction coupled with the conversion of the polyproline-I helix (PPI, having all cis-configured peptide bonds) into polyproline-II (PPII, all trans) helix is observed in this work. Kinetics and equilibrium measurements as a function of temperature allow determination of the thermochemistry and insight into how proton transfer is regulated in this system. For the proton-transfer process, PPI(+)(PrOH) + H3O(+) → PPII(2+)(PrOH/aq) + H2O, we determine ΔG = -20 ± 19 kJ·mol(-1), ΔH = -75 ± 14 kJ·mol(-1), and ΔS= -188 ± 48 J·mol(-1)·K(-1) for the overall reaction, and values of ΔG(⧧) = 91 ± 3 kJ·mol(-1), ΔH(⧧) = 84 ± 9 kJ·mol(-1), and ΔS(⧧) = -23 ± 31 J·mol(-1)·K(-1) for the transition state. For a minor process, PPI(+)(PrOH) → PPII(+)(PrOH/aq) without protonation, we determine ΔG = -9 ± 20 kJ·mol(-1), ΔH = 64 ± 14 kJ·mol(-1), and ΔS= 247 ± 50 J·mol(-1)·K(-1). This thermochemistry yields ΔG = -10 ± 29 kJ·mol(-1), ΔH = -139 ± 20 kJ·mol(-1), and ΔS= -435 ± 70 J·mol(-1)·K(-1) for PPII(+)(PrOH/aq) + H3O(+) → PPII(2+)(PrOH/aq) +H2O. The extraordinarily slow proton transfer appears to be an outcome of configurational coupling through a PPI-like transition state. PMID:26115587

  10. Proton NMR: a convenient method for determining 2-monoacylglycerol acyl migration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The acyl migration kinetics of neat (not exposed to solvent) 2-monoacylglycerol (2-MAG) to form 1-monoacylglycerol (1-MAG) was determined using proton NMR spectroscopy to monitor the B-proton integration ratios of the two species over time. 2-MAG was synthesized by the Novozym 435-catalyzed alcohol...

  11. Improving the resolution in proton-detected through-space heteronuclear multiple quantum correlation NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Shen, Ming; Trébosc, J.; Lafon, O.; Pourpoint, F.; Hu, Bingwen; Chen, Qun; Amoureux, J.-P.

    2014-08-01

    Connectivities and proximities between protons and low-gamma nuclei can be probed in solid-state NMR spectroscopy using two-dimensional (2D) proton-detected heteronuclear correlation, through Heteronuclear Multiple Quantum Correlation (HMQC) pulse sequence. The indirect detection via protons dramatically enhances the sensitivity. However, the spectra are often broadened along the indirect F1 dimension by the decay of heteronuclear multiple-quantum coherences under the strong 1H-1H dipolar couplings. This work presents a systematic comparison of the performances of various decoupling schemes during the indirect t1 evolution period of dipolar-mediated HMQC (D-HMQC) experiment. We demonstrate that 1H-1H dipolar decoupling sequences during t1, such as symmetry-based schemes, phase-modulated Lee-Goldburg (PMLG) and Decoupling Using Mind-Boggling Optimization (DUMBO), provide better resolution than continuous wave 1H irradiation. We also report that high resolution requires the preservation of 1H isotropic chemical shifts during the decoupling sequences. When observing indirectly broad spectra presenting numerous spinning sidebands, the D-HMQC sequence must be fully rotor-synchronized owing to the rotor-synchronized indirect sampling and dipolar recoupling sequence employed. In this case, we propose a solution to reduce artefact sidebands caused by the modulation of window delays before and after the decoupling application during the t1 period. Moreover, we show that 1H-1H dipolar decoupling sequence using Smooth Amplitude Modulation (SAM) minimizes the t1-noise. The performances of the various decoupling schemes are assessed via numerical simulations and compared to 2D 1H-{13C} D-HMQC experiments on [U-13C]-L-histidineṡHClṡH2O at various magnetic fields and Magic Angle spinning (MAS) frequencies. Great resolution and sensitivity enhancements resulting from decoupling during t1 period enable the detection of heteronuclear correlation between aliphatic protons and

  12. Proton NMR of Escherichia coli sulfite reductase: the unligated hemeprotein subunit.

    PubMed

    Kaufman, J; Spicer, L D; Siegel, L M

    1993-03-23

    The isolated hemeprotein subunit of sulfite reductase (SiR-HP) from Escherichia coli consists of a high spin ferric isobacteriochlorin (siroheme) coupled to a diamagnetic [4Fe-4S]2+ cluster. When supplied with an artificial electron donor, such as methyl viologen cation radical, SiR-HP can catalyze the six electron reductions of sulfite to sulfide and nitrite to ammonia. Thus, the hemeprotein subunit appears to represent the minimal protein structure required for multielectron reductase activity. Proton magnetic resonance spectra are reported for the first time on unligated SiR-HP at 300 MHz in all three redox states. The NMR spectrum of high spin ferric siroheme at pH 6.0 was obtained for the purpose of comparing its spectrum with that of oxidized SiR-HP. On the basis of line widths, T1 measurements, and 1D NOE experiments, preliminary assignments have been made for the oxidized enzyme in solution. The pH profile of oxidized SiR-HP is unusual in that a single resonance shows a 9 ppm shift over a range of only 3 pH units with an apparent pK = 6.7 +/- 0.2. Resonances arising from the beta-CH2 protons of cluster cysteines have been assigned using deuterium substitution for all redox states. One beta-CH2 resonance has been tentatively assigned to the bridging cysteine on the basis of chemical shift, T1, line width, and the presence of NOEs to protons from the siroheme ring. The observed pattern of hyperfine shifts can be used as a probe to measure the degree of coupling between siroheme and cluster in solution. The cluster iron sites of the resting (oxidized) enzyme are found to possess both positive and negative spin density which is in good agreement with Mossbauer results on frozen enzyme. The NMR spectrum of the 1-electron reduced form of SiR-HP is consistent with an intermediate spin (S = 1) siroheme. Intermediate spin Fe(II) hemes have only been previously observed in 4-coordinate model compounds. However, the amount of electron density transferred to the

  13. Proton NMR Spectra: Deceptively Simple and Deceptively Complex Examples.

    ERIC Educational Resources Information Center

    Gurst, J. E.; And Others

    1985-01-01

    Describes relatively simple nuclear magnetic resonance (NMR) experiments that demonstrate unexpected results of the deceptively simple and deceptively complex types. Background information, experimental procedures, and typical results obtained are included. (JN)

  14. Development and application of proton NMR methodology to lipoprotein analysis

    NASA Astrophysics Data System (ADS)

    Korhonen, Ari Juhani

    1998-11-01

    The present thesis describes the development of 1H NMR spectroscopy and its applications to lipoprotein analysis in vitro, utilizing biochemical prior knowledge and advanced lineshape fitting analysis in the frequency domain. A method for absolute quantification of lipoprotein lipids and proteins directly from the terminal methyl-CH3 resonance region of 1H NMR spectra of human blood plasma is described. Then the use of NMR methodology in time course studies of the oxidation process of LDL particles is presented. The function of the cholesteryl ester transfer protein (CETP) in lipoprotein mixtures was also assessed by 1H NMR, which allows for dynamic follow-up of the lipid transfer reactions between VLDL, LDL, and HDL particles. The results corroborated the suggestion that neutral lipid mass transfer among lipoproteins is not an equimolar heteroexchange. A novel method for studying lipoprotein particle fusion is also demonstrated. It is shown that the progression of proteolytically (α- chymotrypsin) induced fusion of LDL particles can be followed by 1H NMR spectroscopy and, moreover, that fusion can be distinguished from aggregation. In addition, NMR methodology was used to study the changes in HDL3 particles induced by phospholipid transfer protein (PLTP) in HDL3 + PLTP mixtures. The 1H NMR study revealed a gradual production of enlarged HDL particles, which demonstrated that PLTP-mediated remodeling of HDL involves fusion of the HDL particles. These applications demonstrated that the 1H NMR approach offers several advantages both in quantification and in time course studies of lipoprotein-lipoprotein interactions and of enzyme/lipid transfer protein function.

  15. Heteronuclear dipolar couplings, total spin coherence, and bilinear rotations in NMR spectroscopy

    SciTech Connect

    Garbow, J.R.

    1983-07-01

    In Chapter 1 a variety of different introductory topics are presented. The potential complexity of the nuclear magnetic resonsnace (NMR) spectra of molecules dissolved in liquid crystal solvents serves to motivate the development of multiple quantum (MQ) spectroscopy. The basics of MQ NMR are reviewed in Chapter 2. An experimental search procedure for the optimization of MQ pulse sequences is introduced. Chapter 3 discusses the application of MQ NMR techniques to the measurement of dipolar couplings in heteronuclear spin systems. The advantages of MQ methods in such systems are developed and experimental results for partially oriented (1-/sup 13/C) benzene are presented. Several pulse sequences are introduced which employ a two-step excitation of heteronuclear MQ coherence. A new multiple pulse method, involving the simultaneous irradiation of both rare and abundant spin species, is described. The problem of the broadening of MQ transitions due to magnetic field inhomogeneity is considered in Chapter 4. The method of total spin coherence transfer echo spectroscopy (TSCTES) is presented, with experimets on partially oriented acetaldehyde serving to demonstrate this new technique. TSCTES results in MQ spectra which are sensitive to all chemical shifts and spin-spin couplings and which are free of inhomogeneous broadening. In Chapter 5 the spectroscopy of spin systems of several protons and a /sup 13/C nucleus in the isotropic phase is discussed. The usefulness of the heteronuclear bilinear rotation as a calculational tool is illustrated. Compensated bilinear ..pi.. rotations, which are relatively insensitive to timing parameter missets, are presented. A new technique for homonuclear proton decoupling, Bilinear Rotation Decoupling, is described and its success in weakly coupled systems is demonstrated.

  16. Operando NMR spectroscopic analysis of proton transfer in heterogeneous photocatalytic reactions

    PubMed Central

    Wang, Xue Lu; Liu, Wenqing; Yu, Yan-Yan; Song, Yanhong; Fang, Wen Qi; Wei, Daxiu; Gong, Xue-Qing; Yao, Ye-Feng; Yang, Hua Gui

    2016-01-01

    Proton transfer (PT) processes in solid–liquid phases play central roles throughout chemistry, biology and materials science. Identification of PT routes deep into the realistic catalytic process is experimentally challenging, thus leaving a gap in our understanding. Here we demonstrate an approach using operando nuclear magnetic resonance (NMR) spectroscopy that allows to quantitatively describe the complex species dynamics of generated H2/HD gases and liquid intermediates in pmol resolution during photocatalytic hydrogen evolution reaction (HER). In this system, the effective protons for HER are mainly from H2O, and CH3OH evidently serves as an outstanding sacrificial agent reacting with holes, further supported by our density functional theory calculations. This results rule out controversy about the complicated proton sources for HER. The operando NMR method provides a direct molecular-level insight with the methodology offering exciting possibilities for the quantitative studies of mechanisms of proton-involved catalytic reactions in solid–liquid phases. PMID:27311326

  17. Operando NMR spectroscopic analysis of proton transfer in heterogeneous photocatalytic reactions.

    PubMed

    Wang, Xue Lu; Liu, Wenqing; Yu, Yan-Yan; Song, Yanhong; Fang, Wen Qi; Wei, Daxiu; Gong, Xue-Qing; Yao, Ye-Feng; Yang, Hua Gui

    2016-01-01

    Proton transfer (PT) processes in solid-liquid phases play central roles throughout chemistry, biology and materials science. Identification of PT routes deep into the realistic catalytic process is experimentally challenging, thus leaving a gap in our understanding. Here we demonstrate an approach using operando nuclear magnetic resonance (NMR) spectroscopy that allows to quantitatively describe the complex species dynamics of generated H2/HD gases and liquid intermediates in pmol resolution during photocatalytic hydrogen evolution reaction (HER). In this system, the effective protons for HER are mainly from H2O, and CH3OH evidently serves as an outstanding sacrificial agent reacting with holes, further supported by our density functional theory calculations. This results rule out controversy about the complicated proton sources for HER. The operando NMR method provides a direct molecular-level insight with the methodology offering exciting possibilities for the quantitative studies of mechanisms of proton-involved catalytic reactions in solid-liquid phases. PMID:27311326

  18. Amide proton exchange rates of a bound pepsin inhibitor determined by isotope-edited proton NMR experiments

    SciTech Connect

    Fesik, S.W.; Luly, J.R.; Stein, H.H.; BaMaung, N.

    1987-09-30

    From a series of isotope-edited proton NMR spectra, amide proton exchange rates were measured at 20 C, 30 C, and 40/sup 0/C for a tightly bound /sup 15/N-labeled tripeptide inhibitor of porcine pepsin (IC50 = 1.7 X 10(-) M). Markedly different NH exchange rates were observed for the three amide protons of the bound inhibitor. The P1 NH exchanged much more slowly than the P2 NH and P3 NH. These results are discussed in terms of the relative solvent accessibility in the active site and the role of the NH protons of the inhibitor for hydrogen bonding to the enzyme. In this study a useful approach is demonstrated for obtaining NH exchange rates on ligands bound to biomacromolecules, the knowledge of which could be of potential utility in the design of therapeutically useful nonpeptide enzyme inhibitors from peptide leads.

  19. Novel macrocyclic carriers for proton-coupled liquid membrane transport

    SciTech Connect

    Lamb, J.D.

    1991-06-10

    The objective of our research program is to elucidate the chemical principles which are responsible for the cation selectivity and permeability of liquid membranes containing macrocyclic carriers. Several new macrocyclic carriers were synthesized during the last three year period, including selenium-containing macrocycles, new crown-4 structures, and several new crown structures containing nitrogen based heterocycles as substituents in the principal macrocyclic ring. The cation binding properties of these macrocycles were investigated by potentiometric titration, calorimetric titration, solvent extraction, and NMR techniques. In addition, hydrophobic macrocycles were incorporated into dual hollow fiber membrane systems to investigate their membrane performance, especially in the proton-coupled transport mode. It was found that the dual hollow fiber system maintains the cation selectivity and permeability of supported liquid membranes, while enhancing membrane stability. The diffusion limited transport model was expanded to account for membrane solvent effects. Furthermore, Eu{sup 2+} transport was found to be similar to that of strontium and much higher than that of the lanthanides, in supported liquid membrane systems.

  20. Solid-state NMR analysis of membrane proteins and protein aggregates by proton detected spectroscopy

    PubMed Central

    Nieuwkoop, Andrew J.; Berthold, Deborah A.; Comellas, Gemma; Sperling, Lindsay J.; Tang, Ming; Shah, Gautam J.; Brea, Elliott J.; Lemkau, Luisel R.

    2012-01-01

    Solid-state NMR has emerged as an important tool for structural biology and chemistry, capable of solving atomic-resolution structures for proteins in membrane-bound and aggregated states. Proton detection methods have been recently realized under fast magic-angle spinning conditions, providing large sensitivity enhancements for efficient examination of uniformly labeled proteins. The first and often most challenging step of protein structure determination by NMR is the site-specific resonance assignment. Here we demonstrate resonance assignments based on high-sensitivity proton-detected three-dimensional experiments for samples of different physical states, including a fully-protonated small protein (GB1, 6 kDa), a deuterated microcrystalline protein (DsbA, 21 kDa), a membrane protein (DsbB, 20 kDa) prepared in a lipid environment, and the extended core of a fibrillar protein (α-synuclein, 14 kDa). In our implementation of these experiments, including CONH, CO(CA)NH, CANH, CA(CO)NH, CBCANH, and CBCA(CO)NH, dipolar-based polarization transfer methods have been chosen for optimal efficiency for relatively high protonation levels (full protonation or 100 % amide proton), fast magic-angle spinning conditions (40 kHz) and moderate proton decoupling power levels. Each H–N pair correlates exclusively to either intra- or inter-residue carbons, but not both, to maximize spectral resolution. Experiment time can be reduced by at least a factor of 10 by using proton detection in comparison to carbon detection. These high-sensitivity experiments are especially important for membrane proteins, which often have rather low expression yield. Proton-detection based experiments are expected to play an important role in accelerating protein structure elucidation by solid-state NMR with the improved sensitivity and resolution. PMID:22986689

  1. Selective excitation enables assignment of proton resonances and {sup 1}H-{sup 1}H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy

    SciTech Connect

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-07-21

    Remarkable developments in ultrafast magic angle spinning (MAS) solid-state NMR spectroscopy enabled proton-based high-resolution multidimensional experiments on solids. To fully utilize the benefits rendered by proton-based ultrafast MAS experiments, assignment of {sup 1}H resonances becomes absolutely necessary. Herein, we propose an approach to identify different proton peaks by using dipolar-coupled heteronuclei such as {sup 13}C or {sup 15}N. In this method, after the initial preparation of proton magnetization and cross-polarization to {sup 13}C nuclei, transverse magnetization of desired {sup 13}C nuclei is selectively prepared by using DANTE (Delays Alternating with Nutations for Tailored Excitation) sequence and then, it is transferred to bonded protons with a short-contact-time cross polarization. Our experimental results demonstrate that protons bonded to specific {sup 13}C atoms can be identified and overlapping proton peaks can also be assigned. In contrast to the regular 2D HETCOR experiment, only a few 1D experiments are required for the complete assignment of peaks in the proton spectrum. Furthermore, the finite-pulse radio frequency driven recoupling sequence could be incorporated right after the selection of specific proton signals to monitor the intensity buildup for other proton signals. This enables the extraction of {sup 1}H-{sup 1}H distances between different pairs of protons. Therefore, we believe that the proposed method will greatly aid in fast assignment of peaks in proton spectra and will be useful in the development of proton-based multi-dimensional solid-state NMR experiments to study atomic-level resolution structure and dynamics of solids.

  2. Selective excitation enables assignment of proton resonances and (1)H-(1)H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy.

    PubMed

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-07-21

    Remarkable developments in ultrafast magic angle spinning (MAS) solid-state NMR spectroscopy enabled proton-based high-resolution multidimensional experiments on solids. To fully utilize the benefits rendered by proton-based ultrafast MAS experiments, assignment of (1)H resonances becomes absolutely necessary. Herein, we propose an approach to identify different proton peaks by using dipolar-coupled heteronuclei such as (13)C or (15)N. In this method, after the initial preparation of proton magnetization and cross-polarization to (13)C nuclei, transverse magnetization of desired (13)C nuclei is selectively prepared by using DANTE (Delays Alternating with Nutations for Tailored Excitation) sequence and then, it is transferred to bonded protons with a short-contact-time cross polarization. Our experimental results demonstrate that protons bonded to specific (13)C atoms can be identified and overlapping proton peaks can also be assigned. In contrast to the regular 2D HETCOR experiment, only a few 1D experiments are required for the complete assignment of peaks in the proton spectrum. Furthermore, the finite-pulse radio frequency driven recoupling sequence could be incorporated right after the selection of specific proton signals to monitor the intensity buildup for other proton signals. This enables the extraction of (1)H-(1)H distances between different pairs of protons. Therefore, we believe that the proposed method will greatly aid in fast assignment of peaks in proton spectra and will be useful in the development of proton-based multi-dimensional solid-state NMR experiments to study atomic-level resolution structure and dynamics of solids. PMID:26203019

  3. Selective excitation enables assignment of proton resonances and 1H-1H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-07-01

    Remarkable developments in ultrafast magic angle spinning (MAS) solid-state NMR spectroscopy enabled proton-based high-resolution multidimensional experiments on solids. To fully utilize the benefits rendered by proton-based ultrafast MAS experiments, assignment of 1H resonances becomes absolutely necessary. Herein, we propose an approach to identify different proton peaks by using dipolar-coupled heteronuclei such as 13C or 15N. In this method, after the initial preparation of proton magnetization and cross-polarization to 13C nuclei, transverse magnetization of desired 13C nuclei is selectively prepared by using DANTE (Delays Alternating with Nutations for Tailored Excitation) sequence and then, it is transferred to bonded protons with a short-contact-time cross polarization. Our experimental results demonstrate that protons bonded to specific 13C atoms can be identified and overlapping proton peaks can also be assigned. In contrast to the regular 2D HETCOR experiment, only a few 1D experiments are required for the complete assignment of peaks in the proton spectrum. Furthermore, the finite-pulse radio frequency driven recoupling sequence could be incorporated right after the selection of specific proton signals to monitor the intensity buildup for other proton signals. This enables the extraction of 1H-1H distances between different pairs of protons. Therefore, we believe that the proposed method will greatly aid in fast assignment of peaks in proton spectra and will be useful in the development of proton-based multi-dimensional solid-state NMR experiments to study atomic-level resolution structure and dynamics of solids.

  4. High resolution NMR study of T{sub 1} magnetic relaxation dispersion. IV. Proton relaxation in amino acids and Met-enkephalin pentapeptide

    SciTech Connect

    Pravdivtsev, Andrey N.; Yurkovskaya, Alexandra V.; Ivanov, Konstantin L.; Vieth, Hans-Martin

    2014-10-21

    Nuclear Magnetic Relaxation Dispersion (NMRD) of protons was studied in the pentapeptide Met-enkephalin and the amino acids, which constitute it. Experiments were run by using high-resolution Nuclear Magnetic Resonance (NMR) in combination with fast field-cycling, thus enabling measuring NMRD curves for all individual protons. As in earlier works, Papers I–III, pronounced effects of intramolecular scalar spin-spin interactions, J-couplings, on spin relaxation were found. Notably, at low fields J-couplings tend to equalize the apparent relaxation rates within networks of coupled protons. In Met-enkephalin, in contrast to the free amino acids, there is a sharp increase in the proton T{sub 1}-relaxation times at high fields due to the changes in the regime of molecular motion. The experimental data are in good agreement with theory. From modelling the relaxation experiments we were able to determine motional correlation times of different residues in Met-enkephalin with atomic resolution. This allows us to draw conclusions about preferential conformation of the pentapeptide in solution, which is also in agreement with data from two-dimensional NMR experiments (rotating frame Overhauser effect spectroscopy). Altogether, our study demonstrates that high-resolution NMR studies of magnetic field-dependent relaxation allow one to probe molecular mobility in biomolecules with atomic resolution.

  5. Interactions between Nafion resin and protonated dodecylamine modified montmorillonite: a solid state NMR study.

    PubMed

    Zhang, Limin; Xu, Jun; Hou, Guangjin; Tang, Huiru; Deng, Feng

    2007-07-01

    A series of nanocomposites have been prepared from perfluorosulfonylfluoride copolymer resin (Nafion) and layered montmorillonite (MMT) modified with protonated dodecylamine by conventional sol-gel intercalation. The structure of these nanocomposite materials have been characterized using FT-IR, elemental analysis, XRD and solid state NMR techniques, including 19F magic-angle spinning (MAS) NMR, 19F NMR relaxation time measurements, 29Si MAS, 1H MAS, 1H-13C cross-polarization magic-angle spinning (CPMAS), and 1H-13C heteronuclear correlation (HETCOR) 2D NMR. The results showed that thermal stability of Nafion was improved moderately by the addition of dodecylamine modified MMT without intercalation. FT-IR and 29Si MAS NMR results indicated that dodecylamine modification did not result in obvious changes in the MMT lattice structure. The XRD results showed that the protonated dodecylamine has been embedded and intercalated into the MMT interlayers, whereas Nafion was not. Elemental analysis results also suggested that some dodecylamine was adsorbed on the surface of MMT. 1H-13C HETCOR 2D NMR experiment clearly indicated that strong electrostatic interactions were present between the NH+3 group of dodecylamine and the fluorine-containing groups (CF3, OCF2, and SCF2) of Nafion resin. Such electrostatic interactions are probably the major contributors for the improved thermal stability of the resultant composite materials. PMID:17382953

  6. Magnetic couplings in the chemical shift of paramagnetic NMR.

    PubMed

    Vaara, Juha; Rouf, Syed Awais; Mareš, Jiří

    2015-10-13

    We apply the Kurland-McGarvey (J. Magn. Reson. 1970, 2, 286) theory for the NMR shielding of paramagnetic molecules, particularly its special case limited to the ground-state multiplet characterized by zero-field splitting (ZFS) interaction of the form S·D·S. The correct formulation for this problem was recently presented by Soncini and Van den Heuvel (J. Chem. Phys. 2013, 138, 054113). With the effective electron spin quantum number S, the theory involves 2S+1 states, of which all but one are low-lying excited states, between which magnetic couplings take place by Zeeman and hyperfine interactions. We investigate these couplings as a function of temperature, focusing on both the high- and low-temperature behaviors. As has been seen in work by others, the full treatment of magnetic couplings is crucial for a realistic description of the temperature behavior of NMR shielding up to normal measurement temperatures. At high temperatures, depending on the magnitude of ZFS, the effect of magnetic couplings diminishes, and the Zeeman and hyperfine interactions become effectively averaged in the thermally occupied states of the multiplet. At still higher temperatures, the ZFS may be omitted altogether, and the shielding properties may be evaluated using a doublet-like formula, with all the 2S+1 states becoming effectively degenerate at the limit of vanishing magnetic field. We demonstrate these features using first-principles calculations of Ni(II), Co(II), Cr(II), and Cr(III) complexes, which have ZFS of different sizes and signs. A non-monotonic inverse temperature dependence of the hyperfine shift is predicted for axially symmetric integer-spin systems with a positive D parameter of ZFS. This is due to the magnetic coupling terms that are proportional to kT at low temperatures, canceling the Curie-type 1/kT prefactor of the hyperfine shielding in this case. PMID:26574272

  7. Proton NMR study of the state of water in fibrin gels, plasma, and blood clots

    SciTech Connect

    Blinc, A.; Lahajnar, G.; Blinc, R.; Zidansek, A.; Sepe, A. )

    1990-04-01

    A proton NMR relaxation and pulsed field gradient self-diffusion study of water in fibrin gels, plasma, and blood clots has been performed with special emphasis on the effect of the sol-gel and shrinkage transitions. Deuteron NMR in fibrin gels was also studied to supplement the proton data. It is shown that a measurement of the water proton or deuteron T1/T2 ratio allows for a determination of the bound water fraction in all these systems. The change in the T1/T2 ratio at the shrinkage transition further allows for a determination of the surface fractal dimension of the gel if the change in the volume of the gel is known. The self-diffusion coefficient of water in these systems, which determines the transport properties of the gel, is found to be proportional to the free water fraction in both the nonshrunken and shrunken state.

  8. Theoretical analysis of proton relays in electrochemical proton-coupled electron transfer.

    PubMed

    Auer, Benjamin; Fernandez, Laura E; Hammes-Schiffer, Sharon

    2011-06-01

    The coupling of long-range electron transfer to proton transport over multiple sites plays a vital role in many biological and chemical processes. Recently the concerted proton-coupled electron transfer (PCET) reaction in a molecule with a hydrogen-bond relay inserted between the proton donor and acceptor sites was studied electrochemically. The standard rate constants and kinetic isotope effects (KIEs) were measured experimentally for this double proton transfer system and a related single proton transfer system. In the present paper, these systems are studied theoretically using vibronically nonadiabatic rate constant expressions for electrochemical PCET. Application of this approach to proton relays requires the calculation of multidimensional proton vibrational wave functions and the incorporation of multiple proton donor-acceptor motions. The decrease in proton donor-acceptor distances due to thermal fluctuations and the contributions from excited electron-proton vibronic states play important roles in these systems. The calculated KIEs and the ratio of the standard rate constants for the single and double proton transfer systems are in agreement with the experimental data. The calculations indicate that the standard PCET rate constant is lower for the double proton transfer system because of the smaller overlap integral between the ground state reduced and oxidized proton vibrational wave functions, resulting in greater contributions from excited electron-proton vibronic states with higher free energy barriers. The theory predicts that this rate constant may be increased by modifying the molecule in a manner that decreases the equilibrium proton donor-acceptor distances or alters the molecular thermal motions to facilitate the concurrent decrease of these distances. These insights may guide the design of more efficient catalysts for energy conversion devices. PMID:21524104

  9. Proton NMR study of spin dynamics in the magnetic organic chains M (hfac)3 NITEt (M =Eu3 +,Gd3 + )

    NASA Astrophysics Data System (ADS)

    Mariani, M.; Lascialfari, A.; Caneschi, A.; Ammannato, L.; Gatteschi, D.; Rettori, A.; Pini, M. G.; Cucci, C.; Borsa, F.

    2016-04-01

    In this work, we present a nuclear magnetic resonance (NMR) study of the spin dynamics in the rare-earth-based low-dimensional molecular magnetic chains Eu (hfac) 3NITEt and Gd (hfac) 3NITEt (in short, Eu-Et and Gd-Et). Although both samples are based on the same chemical building block, [(hfac) 3NITEt ] , their magnetic properties change dramatically when the Eu3 + ion, which is nonmagnetic at low temperatures, is substituted by the magnetic Gd3 + ion. The present proton NMR investigation shows that, down to the lowest investigated temperature (T =1.5 K for Gd-Et and T =3 K for Eu-Et), the Eu-Et chain behaves as a one-dimensional Heisenberg model with antiferromagnetic exchange coupling (J =-20 K) between s =1 /2 organic radicals, and has a T -independent exchange frequency (ωe=2.6 ×1012 rad/s). In the Gd-Et chain, in contrast, a competition arises between nearest-neighbor ferromagnetic coupling and next-nearest-neighbor antiferromagnetic coupling; moreover, two phase transitions have previously been found, in agreement with Villain's conjecture: a first transition, at T0=2.2 K, from a high temperature paramagnetic phase to a chiral spin liquid phase, and a second transition, at TN=1.9 K, to a three-dimensional helical spin solid phase. Contrary to the Eu-Et chain (whose three-dimensional ordering temperature is estimated to insurge at very low, TN≈0.3 K), critical spin dynamics effects have been measured in the Gd-Et chain on approaching TN=1.9 K: namely, a divergence of the proton nuclear spin-lattice relaxation rate 1 /T1 , which in turn produces a sudden wipe-out of the NMR signal in a very narrow (Δ T ˜0.04 K) temperature range above TN. Below TN, an inhomogeneous broadening of the NMR line indicates a complete spin freezing. At T0=2.2 K, instead, such critical effects are not observed because NMR measurements probe the two-spin correlation function, while the chiral spin liquid phase transition is associated with a divergence of the four

  10. Fluorine-19 NMR of solids with both homonuclear (multipulse) decoupling and pulsed proton decoupling

    NASA Astrophysics Data System (ADS)

    Scheler, Ulrich; Harris, Robin K.

    1996-11-01

    The application of multipulse and of combined rotation and multipulse spectroscopy (CRAMPS) to fluorine is demonstrated. The MREV-8 multipulse sequence is applied to average the homonuclear dipolar coupling between the fluorine nuclei. The heteronuclear dipolar coupling to the protons can be suppressed by irradiation with a synchronized sequence of π pulses at the proton frequency. MAS is applied to average the anisotropy of the chemical shift. Applications to a fluorinated adamantane derivative and to polyvinylidenedifluoride (PVDF) are shown.

  11. NMR studies of protonation and hydrogen bond states of internal aldimines of pyridoxal 5'-phosphate acid-base in alanine racemase, aspartate aminotransferase, and poly-L-lysine.

    PubMed

    Chan-Huot, Monique; Dos, Alexandra; Zander, Reinhard; Sharif, Shasad; Tolstoy, Peter M; Compton, Shara; Fogle, Emily; Toney, Michael D; Shenderovich, Ilya; Denisov, Gleb S; Limbach, Hans-Heinrich

    2013-12-01

    Using (15)N solid-state NMR, we have studied protonation and H-bonded states of the cofactor pyridoxal 5'-phosphate (PLP) linked as an internal aldimine in alanine racemase (AlaR), aspartate aminotransferase (AspAT), and poly-L-lysine. Protonation of the pyridine nitrogen of PLP and the coupled proton transfer from the phenolic oxygen (enolimine form) to the aldimine nitrogen (ketoenamine form) is often considered to be a prerequisite to the initial step (transimination) of the enzyme-catalyzed reaction. Indeed, using (15)N NMR and H-bond correlations in AspAT, we observe a strong aspartate-pyridine nitrogen H-bond with H located on nitrogen. After hydration, this hydrogen bond is maintained. By contrast, in the case of solid lyophilized AlaR, we find that the pyridine nitrogen is neither protonated nor hydrogen bonded to the proximal arginine side chain. However, hydration establishes a weak hydrogen bond to pyridine. To clarify how AlaR is activated, we performed (13)C and (15)N solid-state NMR experiments on isotopically labeled PLP aldimines formed by lyophilization with poly-L-lysine. In the dry solid, only the enolimine tautomer is observed. However, a fast reversible proton transfer involving the ketoenamine tautomer is observed after treatment with either gaseous water or gaseous dry HCl. Hydrolysis requires the action of both water and HCl. The formation of an external aldimine with aspartic acid at pH 9 also produces the ketoenamine form stabilized by interaction with a second aspartic acid, probably via a H-bond to the phenolic oxygen. We postulate that O-protonation is an effectual mechanism for the activation of PLP, as is N-protonation, and that enzymes that are incapable of N-protonation employ this mechanism. PMID:24147985

  12. Analysis of human muscle extracts by proton NMR

    SciTech Connect

    Venkatasubramanian, P.N.; Barany, M.; Arus, C.

    1986-03-01

    Perchloric acid extracts were prepared from pooled human muscle biopsies from patients diagnosed with scoliosis (SCOL) and cerebral palsy (CP). After neutralization with KOH and removal of perchlorate, the extracts were concentrated by freeze drying and dissolved in /sup 2/H/sub 2/O to contain 120 O.D. units at 280 nm per 0.5 ml. /sup 1/H NMR spectroscopy was performed with the 5 mm probe of a Varian XL300 instrument. Creatine, lactate, carnosine, and choline were the major resonances in the one-dimensional spectra of both extracts. With creatine as reference, 2.5-fold more lactate was found in SCOL than in CP, and a much smaller difference was also found in their carnosine content. Two-dimensional COSY comparison revealed several differences between the two extracts. Taurine, N-acetyl glutamate, glycerophosphoryl choline (or phosphoryl choline) and an unidentified spot were present only in the extract from SCOL but not in that from CP. On the other hand, aspartate, hydroxy-proline, carnitine and glycerophosphoryl ethanolamine were only present in CP but absent in SCOL. Alanine, cysteine, lysine and arginine appeared in both extracts without an apparent intensity difference.

  13. Non-destructive ripeness sensing by using proton NMR (Nuclear Magnetic Resonance)

    SciTech Connect

    Cho, Seong In; Krutz, G.W.; Stroshine, R.L. . Dept. of Agricultural Engineering); Bellon, V. , 34 - Montpellier )

    1990-01-01

    More than 80 kinds of fruits and vegetables are available in the United States. But only about 6 of them have their quality standards (Dull, 1986). In the 1990 Fresh Trends survey (Zind, 1990), consumers were asked to rate 16 characteristics important to their decision to purchase fresh produce. The four top ranking factors were ripeness/freshness, taste/flavor, appearance/condition and nutritional value. Of these surveyed, 96% rated ripeness/freshness as extremely important or very important. Therefore, the development of reliable grading or sorting techniques for fresh commodities is essential. Determination of fruit quality often involves cutting and tasting. Non-destructive quality control in fruit and vegetables is a goal of growers and distributors, as well as the food processing industry. Many nondestructive techniques have been evaluated including soft x-ray, optical transmission, near infrared radiation, and machine vision. However, there are few reports of successful non-destructive measurement of sugar content directly in fruit. Higher quality fruit could be harvested and available to consumers if a nondestructive sensor that detects ripeness level directly by measuring sugar content were available. Using proton Nuclear Magnetic Resonance (NMR) principle is the possibility. A nondestructive ripeness (or sweetness) sensor for fruit quality control can be developed with the proton NMR principle (Cho, 1989). Several feasibility studies were necessary for the ripeness sensor development. Main objectives in this paper was to investigate the feasibilities (1) to detect ripeness (or sweetness level) of raw fruit tissue with an high resolution proton NMR spectroscopy (200 MHz) and (2) to measure sugar content of intact fruit with a low resolution proton NMR spectroscopy (10 MHz). 7 refs., 4 figs.

  14. Non-destructive Ripeness Sensing by Using Proton NMR [Nuclear Magnetic Resonance

    DOE R&D Accomplishments Database

    Cho, Seong In; Krutz, G. W.; Stroshine, R. L.; Bellon, V.

    1990-01-01

    More than 80 kinds of fruits and vegetables are available in the United States. But only about 6 of them have their quality standards (Dull, 1986). In the 1990 Fresh Trends survey (Zind, 1990), consumers were asked to rate 16 characteristics important to their decision to purchase fresh produce. The four top ranking factors were ripeness/freshness, taste/flavor, appearance/condition and nutritional value. Of these surveyed, 96% rated ripeness/freshness as extremely important or very important. Therefore, the development of reliable grading or sorting techniques for fresh commodities is essential. Determination of fruit quality often involves cutting and tasting. Non-destructive quality control in fruit and vegetables is a goal of growers and distributors, as well as the food processing industry. Many nondestructive techniques have been evaluated including soft x-ray, optical transmission, near infrared radiation, and machine vision. However, there are few reports of successful non-destructive measurement of sugar content directly in fruit. Higher quality fruit could be harvested and available to consumers if a nondestructive sensor that detects ripeness level directly by measuring sugar content were available. Using proton Nuclear Magnetic Resonance (NMR) principle is the possibility. A nondestructive ripeness (or sweetness) sensor for fruit quality control can be developed with the proton NMR principle (Cho, 1989). Several feasibility studies were necessary for the ripeness sensor development. Main objectives in this paper was to investigate the feasibilities (1) to detect ripeness (or sweetness level) of raw fruit tissue with an high resolution proton NMR spectroscopy (200 MHz) and (2) to measure sugar content of intact fruit with a low resolution proton NMR spectroscopy (10 MHz).

  15. Solid-state proton multiple-quantum NMR spectroscopy with fast magic angle spinning

    NASA Astrophysics Data System (ADS)

    Geen, Helen; Titman, Jeremy J.; Gottwald, Johannes; Spiess, Hans W.

    1994-09-01

    The feasibility of multiple-quantum NMR spectroscopy with high resolution for protons in solids is explored. A new multiple-quantum excitation sequence suitable for use with fast magic angle spinning is described, and its performance is compared to that of both static and slow-spinning multiple-quantum methods. Modified sequences with scale the rate of development of the multiple-quantum coherences are also demonstrated, and two-dimensional double-quantum spectra of adamantane and polycarbonate are presented.

  16. Line Narrowing in Solid-State Proton NMR with Acquisition Delay

    NASA Astrophysics Data System (ADS)

    Fung, B. M.; Tong, Tat-Hung; Dollase, Thilo; Magnuson, Matthew L.

    Organic solids have extensive proton-proton dipolar interactions, and their 1H NMR linewidths are very large even with magic-angle spinning at moderate speeds. Recently it has been shown that substantial narrowing of the proton linewidths of organic solids can be achieved by using single-pulse excitation with acquisition delay or spin echo [S. Ding and C. A. McDowell, J. Magn. Reson. A111, 212 (1994); 115, 141 (1995); 117, 171 (1995)]. This interesting line-narrowing phenomenon has been further examined through the study of several amino acids, their deuterated analogs, and some aromatic compounds. The results confirm that narrow proton peaks are observed with long acquisition delay, and the peaks appear in the appropriate chemical-shift ranges for organic protons (0-10 ppm with respect to tetramethylsilane). However, except for some special cases, the observed peaks cannot be assigned to individual types of protons based on chemical-shift considerations only. To explore the reason for the line narrowing, the effect of acquisition delay on the 19F linewidth of CaF 2was also studied and compared with that on the 1H linewidths of organic solids. It is suggested that the broad proton peak in an organic solid is a superposition of numerous transitions. These transitions have different linewidths, and the narrow peaks in the spectrum remain observable with long acquisition delays.

  17. Proton-Coupled Electron Transfer Reactions with Photometric Bases Reveal Free Energy Relationships for Proton Transfer.

    PubMed

    Eisenhart, Thomas T; Howland, William C; Dempsey, Jillian L

    2016-08-18

    The proton-coupled electron transfer (PCET) oxidation of p-aminophenol in acetonitrile was initiated via stopped-flow rapid-mixing and spectroscopically monitored. For oxidation by ferrocenium in the presence of 7-(dimethylamino)quinoline proton acceptors, both the electron transfer and proton transfer components could be optically monitored in the visible region; the decay of the ferrocenium absorbance is readily monitored (λmax = 620 nm), and the absorbance of the 2,4-substituted 7-(dimethylamino)quinoline derivatives (λmax = 370-392 nm) red-shifts substantially (ca. 70 nm) upon protonation. Spectral analysis revealed the reaction proceeds via a stepwise electron transfer-proton transfer process, and modeling of the kinetics traces monitoring the ferrocenium and quinolinium signals provided rate constants for elementary proton and electron transfer steps. As the pKa values of the conjugate acids of the 2,4-R-7-(dimethylamino)quinoline derivatives employed were readily tuned by varying the substituents at the 2- and 4-positions of the quinoline backbone, the driving force for proton transfer was systematically varied. Proton transfer rate constants (kPT,2 = (1.5-7.5) × 10(8) M(-1) s(-1), kPT,4 = (0.55-3.0) × 10(7) M(-1) s(-1)) were found to correlate with the pKa of the conjugate acid of the proton acceptor, in agreement with anticipated free energy relationships for proton transfer processes in PCET reactions. PMID:27500804

  18. NMR resonance splitting of urea in stretched hydrogels: proton exchange and (1)H/(2)H isotopologues.

    PubMed

    Kuchel, Philip W; Naumann, Christoph; Chapman, Bogdan E; Shishmarev, Dmitry; Håkansson, Pär; Bacskay, George; Hush, Noel S

    2014-10-01

    Urea at ∼12 M in concentrated gelatin gel, that was stretched, gave (1)H and (2)H NMR spectral splitting patterns that varied in a predictable way with changes in the relative proportions of (1)H2O and (2)H2O in the medium. This required consideration of the combinatorics of the two amide groups in urea that have a total of four protonation/deuteration sites giving rise to 16 different isotopologues, if all the atoms were separately identifiable. The rate constant that characterized the exchange of the protons with water was estimated by back-transformation analysis of 2D-EXSY spectra. There was no (1)H NMR spectral evidence that the chiral gelatin medium had caused in-equivalence in the protons bonded to each amide nitrogen atom. The spectral splitting patterns in (1)H and (2)H NMR spectra were accounted for by intra-molecular scalar and dipolar interactions, and quadrupolar interactions with the electric field gradients of the gelatin matrix, respectively. PMID:25241007

  19. Intrinsic Proton NMR Studies of Mg(OH)2 and Ca(OH)2

    NASA Astrophysics Data System (ADS)

    Itoh, Yutaka; Isobe, Masahiko

    2016-09-01

    We studied the short proton free induction decay signals and the broad 1H NMR spectra of Mg(OH)2 and Ca(OH)2 powders at 77-355 K and 42 MHz using pulsed NMR techniques. Using a Gaussian-type back extrapolation procedure for the obscured data of the proton free induction decay signals, we obtained more precise values of the second moments of the Fourier-transformed broad NMR spectra than those in a previous report [Y. Itoh and M. Isobe, J. Phys. Soc. Jpn. 84, 113601 (2015)] and compared with the theoretical second moments. The decrease in the second moment could not account for the large decrease in the magnitude of the intrinsic proton spin-lattice relaxation rate 1/T1 from Mg(OH)2 to Ca(OH)2. The analysis of 1/T1 ∝ exp(-Eg/kBT) with Eg ˜ 0.01 eV points to a local hopping mechanism, and that of 1/T1 ∝ Tn with n ˜ 0.5 points to an anharmonic rattling mechanism.

  20. Relaxation of water protons in highly concentrated aqueous protein systems studied by 1H NMR spectroscopy.

    PubMed

    Szuminska, K; Gutsze, A; Kowalczyk, A

    2001-01-01

    Concentrated Aqueous Protein Systems, Proton Relaxation Times, Slow Chemical Exchange In this paper we present proton spin-lattice (T1) and spin-spin (T2) relaxation times measured vs. concentration, temperature, pulse interval (tauCPMG) as well as 1H NMR spectral measurements in a wide range of concentrations of bovine serum albumin (BSA) solutions. The anomalous relaxation behaviour of the water protons, similar to that observed in mammalian lenses, was found in the two most concentrated solutions (44% and 46%). The functional dependence of the spin-spin relaxation time vs. tauCPMG pulse interval and the values of the motional activation parameters obtained from the temperature dependencies of spin-lattice relaxation times suggest that the water molecule mobility is reduced in these systems. The slow exchange process on the T2 time scale is proposed to explain the obtained data. The proton spectral measurements support the hypothesis of a slow exchange mechanism in the highest concentrated solutions. From the analysis of the shape of the proton spectra the mean exchange times between bound and bulk water proton groups (tauex) have been estimated for the range of the highest concentrations (30%-46%). The obtained values are of the order of milliseconds assuring that the slow exchange condition is fulfilled in the most concentrated samples. PMID:11837660

  1. Proton NMR investigation of heme and surrounding proton in low-spin cyanide-ligated bacterial hemoglobin from Vitreoscilla.

    PubMed

    Xia, Y; Wu, J; Guang, S; Zhang, H; Liang, S; Shi, Y

    2000-02-01

    (1)H NMR spectra of low-spin cyanide-ligated bacterial hemoglobin from Vitreoscilla (VtHb-CN) are reported. The assignments of the(1)H NMR spectra of VtHb-CN have been made through MCOSY, NOESY, 1D TOE and SUPERWEFT experiments. Almost all resonance peaks of heme and ligated His85 are identified. The spin-lattice relaxation time T (1)'s and the variation relationships of chemical shifts of these peaks with temperature have been acquired, from which the distances between the measured protons and Fe(3+), and the diamagnetic chemical shifts have been acquired, respectively. The ionization constants of pK (a)'s of ligated His85 are determined through pH titration of chemical shift, which is 4.95 for ligated His85 C(2)H proton. The lower pK (a) is attributed to the influence of the Fe(3+) of carrying positive charge and the coordination of His85 and Fe(3+) of heme. PMID:18763116

  2. Thermodynamics of proton transport coupled ATP synthesis.

    PubMed

    Turina, Paola; Petersen, Jan; Gräber, Peter

    2016-06-01

    The thermodynamic H(+)/ATP ratio of the H(+)-ATP synthase from chloroplasts was measured in proteoliposomes after energization of the membrane by an acid base transition (Turina et al. 2003 [13], 418-422). The method is discussed, and all published data obtained with this system are combined and analyzed as a single dataset. This meta-analysis led to the following results. 1) At equilibrium, the transmembrane ΔpH is energetically equivalent to the transmembrane electric potential difference. 2) The standard free energy for ATP synthesis (reference reaction) is ΔG°ref=33.8±1.3kJ/mol. 3) The thermodynamic H(+)/ATP ratio, as obtained from the shift of the ATP synthesis equilibrium induced by changing the transmembrane ΔpH (varying either pHin or pHout) is 4.0±0.1. The structural H(+)/ATP ratio, calculated from the ratio of proton binding sites on the c-subunit-ring in F0 to the catalytic nucleotide binding sites on the β-subunits in F1, is c/β=14/3=4.7. We infer that the energy of 0.7 protons per ATP that flow through the enzyme, but do not contribute to shifting the ATP/(ADP·Pi) ratio, is used for additional processes within the enzyme, such as activation, and/or energy dissipation, due e.g. to internal uncoupling. The ratio between the thermodynamic and the structural H(+)/ATP values is 0.85, and we conclude that this value represents the efficiency of the chemiosmotic energy conversion within the chloroplast H(+)-ATP synthase. PMID:26940516

  3. Proton-detected solid-state NMR spectroscopy of fully protonated proteins at slow to moderate magic-angle spinning frequencies

    NASA Astrophysics Data System (ADS)

    Mote, Kaustubh R.; Madhu, Perunthiruthy K.

    2015-12-01

    1H -detection offers a substitute to the sensitivity-starved experiments often used to characterize biomolecular samples using magic-angle spinning solid-state NMR spectroscopy (MAS-ssNMR). To mitigate the effects of the strong 1H -1H dipolar coupled network that would otherwise severely broaden resonances, high MAS frequencies (>40 kHz) are often employed. Here, we have explored the alternative of stroboscopic 1H -detection at moderate MAS frequencies of 5-30 kHz using windowed version of supercycled-phase-modulated Lee-Goldburg homonuclear decoupling. We show that improved resolution in the 1H dimension, comparable to that obtainable at high spinning frequencies of 40-60 kHz without homonuclear decoupling, can be obtained in these experiments for fully protonated proteins. Along with detailed analysis of the performance of the method on the standard tri-peptide f-MLF, experiments on micro-crystalline GB1 and amyloid- β aggregates are used to demonstrate the applicability of these pulse-sequences to challenging biomolecular systems. With only two parameters to optimize, broadbanded performance of the homonuclear decoupling sequence, linear dependence of the chemical-shift scaling factor on resonance offset and a straightforward implementation under experimental conditions currently used for many biomolecular studies (viz. spinning frequencies and radio-frequency amplitudes), we expect these experiments to complement the current 13C -detection based methods in assignments and characterization through chemical-shift mapping.

  4. Temperature dependence of proton NMR relaxation times at earth's magnetic field

    NASA Astrophysics Data System (ADS)

    Niedbalski, Peter; Kiswandhi, Andhika; Parish, Christopher; Ferguson, Sarah; Cervantes, Eduardo; Oomen, Anisha; Krishnan, Anagha; Goyal, Aayush; Lumata, Lloyd

    The theoretical description of relaxation processes for protons, well established and experimentally verified at conventional nuclear magnetic resonance (NMR) fields, has remained untested at low fields despite significant advances in low field NMR technology. In this study, proton spin-lattice relaxation (T1) times in pure water and water doped with varying concentrations of the paramagnetic agent copper chloride have been measured from 6 to 92oC at earth's magnetic field (1700 Hz). Results show a linear increase of T1 with temperature for each of the samples studied. Increasing the concentration of the copper chloride greatly reduced T1 and reduced dependence on temperature. The consistency of the results with theory is an important confirmation of past results, while the ability of an ultra-low field NMR system to do contrast-enhanced magnetic resonance imaging (MRI) is promising for future applicability to low-cost medical imaging and chemical identification. This work is supported by US Dept of Defense Award No. W81XWH-14-1-0048 and the Robert A. Welch Foundation Grant No. AT-1877.

  5. A Reinvestigation of Ramsey's Theory of NMR Coupling

    NASA Astrophysics Data System (ADS)

    Ajith Perera, S.; Bartlett, Rodney J.

    A systematic development of relativistic molecular Hamiltonians and various non-relativistic approximations are presented. Our starting point is the Dirac one-fermion Hamiltonian in the presence of an external electromagnetic field. The problems associated with generalizing [`]Dirac's one-fermion theory' smoothly to more than one fermion are discussed. The description of many-fermion systems within the framework of quantum electrodynamics (QED) will lead to Hamiltonians which do not suffer from the problems associated with the direct extension of [`]Dirac's one-fermion theory' to many-fermion system. An exhaustive discussion of the recent QED developments in the relevant area is not presented, except for cursory remarks for completeness. The non-relativistic form (NRF) of the many-electron relativistic Hamiltonian is developed as the working Hamiltonian. It is used to extract operators for the observables, which represent the response of a molecule to an external electromagnetic radiation field. In this study, our focus is mainly on the operators which eventually were used to calculate the nuclear magnetic resonance (NMR) chemical shifts and indirect nuclear spin-spin coupling constants.

  6. The proton-coupled folate transporter: physiological and pharmacological roles.

    PubMed

    Zhao, Rongbao; Goldman, I David

    2013-12-01

    Recent studies have identified the proton-coupled folate transporter (PCFT) as the mechanism by which folates are absorbed across the apical brush-border membrane of the small intestine and across the basolateral membrane of the choroid plexus into the cerebrospinal fluid. Both processes are defective when there are loss-of-function mutations in this gene as occurs in the autosomal recessive disorder hereditary folate malabsorption. Because this transporter functions optimally at low pH, antifolates are being developed that are highly specific for PCFT in order to achieve selective delivery to malignant cells within the acidic environment of solid tumors. PCFT has a spectrum of affinities for folates and antifolates that narrows and increases at low pH. Residues have been identified that play a role in folate and proton binding, proton coupling, and oscillation of the carrier between its conformational states. PMID:24383099

  7. Evidence for a dipolar-coupled AM system in carnosine in human calf muscle from in vivo 1H NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Schröder, Leif; Bachert, Peter

    2003-10-01

    Spin systems with residual dipolar couplings such as creatine, taurine, and lactate in skeletal muscle tissue exhibit first-order spectra in in vivo 1H NMR spectroscopy at 1.5 T because the coupled protons are represented by (nearly) symmetrized eigenfunctions. The imidazole ring protons (H2, H4) of carnosine are suspected to form also a coupled system. The ring's stiffness could enable a connectivity between these anisochronous protons with the consequence of second-order spectra at low field strength. Our purpose was to study whether this deviation from the Paschen-Back condition can be used to detect the H2-H4 coupling in localized 1D 1H NMR spectra obtained at 1.5 T (64 MHz) from the human calf in a conventional whole-body scanner. As for the hydrogen hyperfine interaction, a Breit-Rabi equation was derived to describe the transition from Zeeman to Paschen-Back regime for two dipolar-coupled protons. The ratio of the measurable coupling strength ( Sk) and the difference in resonance frequencies of the coupled spins (Δ ω) induces quantum-state mixing of various degree upon definition of an appropriate eigenbase of the coupled spin system. The corresponding Clebsch-Gordan coefficients manifest in characteristic energy corrections in the Breit-Rabi formula. These additional terms were used to define an asymmetry parameter of the line positions as a function of Sk and Δ ω. The observed frequency shifts of the resonances were found to be consistent with this parameter within the accuracy achievable in in vivo NMR spectroscopy. Thus it was possible to identify the origin of satellite peaks of H2, H4 and to describe this so far not investigated type of residual dipolar coupling in vivo.

  8. Thermodynamic Study on the Protonation Reactions of Glyphosate in Aqueous Solution: Potentiometry, Calorimetry and NMR spectroscopy.

    PubMed

    Liu, Bijun; Dong, Lan; Yu, Qianhong; Li, Xingliang; Wu, Fengchang; Tan, Zhaoyi; Luo, Shunzhong

    2016-03-10

    Glyphosate [N-(phosphonomethyl)glycine] has been described as the ideal herbicide because of its unique properties. There is some conflicting information concerning the structures and conformations involved in the protonation process of glyphosate. Protonation may influence the chemical and physical properties of glyphosate, modifying its structure and the chemical processes in which it is involved. To better understand the species in solution associated with changes in pH, thermodynamic study (potentiometry, calorimetry and NMR spectroscopy) about the protonation pathway of glyphosate is performed. Experimental results confirmed that the order of successive protonation sites of totally deprotonated glyphosate is phosphonate oxygen, amino nitrogen, and finally carboxylate oxygen. This trend is in agreement with the most recent theoretical work in the literature on the subject ( J. Phys. Chem. A 2015, , 119 , 5241 - 5249 ). The result is important because it confirms that the protonated site of glyphosate in pH range 7-8, is not on the amino but on the phosphonate group instead. This corrected information can improve the understanding of the glyphosate chemical and biochemical action. PMID:26862689

  9. Conformation analysis of d-glucaric acid in deuterium oxide by NMR based on its JHH and JCH coupling constants.

    PubMed

    Enomoto-Rogers, Yukiko; Masaki, Hisaharu; Ito, Tetsuya; Furihata, Kazuo; Iwata, Tadahisa

    2016-07-01

    d-Glucaric acid (GA) is an aldaric acid and consists of an asymmetric acyclic sugar backbone with a carboxyl group positioned at either end of its structure (i.e., the C1 and C6 positions). The purpose of this study was to conduct a conformation analysis of flexible GA as a solution in deuterium oxide by NMR spectroscopy, based on J-resolved conformation analysis using proton-proton ((3) JHH ) and proton-carbon ((2) JCH and (3) JCH ) coupling constants, as well as nuclear overhauser effect spectroscopy (NOESY). The (2) JCH and (3) JCH coupling constants were measured using the J-resolved heteronuclear multiple bond correlation (HMBC) NMR technique. NOESY correlation experiments indicated that H2 and H5 were in close proximity, despite the fact that these protons were separated by too large distance in the fully extended form of the chain structure to provide a NOESY correlation. The validities of the three possible conformers along the three different bonds (i.e., C2C3, C3C4, and C4C5) were evaluated sequentially based on the J-coupling values and the NOESY correlations. The results of these analyses suggested that there were three dominant conformers of GA, including conformer 1, which was H2H3:gauche, H3H4:anti, and H4H5:gauche; conformer 2, which was H2H3:gauche, H3H4:anti, and H4H5:anti; and conformer 3, which was H2H3:gauche, H3H4: gauche, and H4H5:anti. These results also suggested that all three of these conformers exist in equilibrium with each other. Lastly, the results of the current study suggested that the conformational structures of GA in solution were 'bent' rather than being fully extended. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26749401

  10. Correlation of the antimicrobial activity of salicylaldehydes with broadening of the NMR signal of the hydroxyl proton. Possible involvement of proton exchange processes in the antimicrobial activity.

    PubMed

    Elo, Hannu; Kuure, Matti; Pelttari, Eila

    2015-03-01

    Certain substituted salicylaldehydes are potent antibacterial and antifungal agents and some of them merit consideration as potential chemotherapeutic agents against Candida infections, but their mechanism of action has remained obscure. We report here a distinct correlation between broadening of the NMR signal of the hydroxyl proton of salicylaldehydes and their activity against several types of bacteria and fungi. When proton NMR spectra of the compounds were determined using hexadeuterodimethylsulfoxide as solvent and the height of the OH proton signal was measured, using the signal of the aldehyde proton as an internal standard, it was discovered that a prerequisite of potent antimicrobial activity is that the proton signal is either unobservable or relatively very low, i.e. that it is extremely broadened. Thus, none of the congeners whose OH proton signal was high were potent antimicrobial agents. Some congeners that gave a very low OH signal were, however, essentially inactive against the microbes, indicating that although drastic broadening of the OH signal appears to be a prerequisite, also other (so far unknown) factors are needed for high antimicrobial activity. Because broadening of the hydroxyl proton signal is related to the speed of the proton exchange process(es) involving that proton, proton exchange may be involved in the mechanism of action of the compounds. Further studies are needed to analyze the relative importance of different factors (such as electronic effects, strength of the internal hydrogen bond, co-planarity of the ring and the formyl group) that determine the rates of those processes. PMID:25621992

  11. Use of acetimidation in the NMR identification of neurophysin lysine protons

    SciTech Connect

    Sardana, V.; Breslow, E.

    1986-05-01

    Acetimidation of the two lysine residues of neurophysin (NP) results in localized changes in the proton magnetic resonance spectrum, allowing identification of lysine side-chain resonances. Neither peptide-binding nor protein self-association appeared to be significantly altered by acetimidation. Additionally, no significant effect of either peptide-binding or self-association on lysine epsilon-CH/sub 2/ protons was seen. However, dimerization-induced NMR changes in the 1.6-1.8 ppm region, associated with lysine ..beta..,..gamma..,sigma protons, were altered in the acetimidated protein. In particular, while the spectrum of the acetimidated NP monomer was almost identical to that of the native protein, a shoulder at 1.72 ppm in the native protein dimer was shifted upfield in the modified dimer. Additionally the direction of NMR shifts in the 1.6-1.8 ppm region normally associated with peptide binding to the NP dimer appeared to be reversed in the acetimidated protein. Binding-induced and dimerization-induced changes in all other regions of the spectrum were identical in the native and modified proteins. These results suggest that one or both NP lysine residues may be near the dimer subunit interface and indicate an effect of peptide-binding on lysine side-chain environment.

  12. Uncertainty measurement for automated macro program-processed quantitative proton NMR spectra.

    PubMed

    Hays, Patrick A; Schoenberger, Torsten

    2014-11-01

    The evaluation of a fully automated quantitative proton nuclear magnetic resonance spectroscopy (qNMR) processing program, including the determination of its processing uncertainty, and the calculations of the combined uncertainty of the qNMR result, is presented with details on the use of a trimmed purity average. Quantitative NMR spectra (1359) were collected over a 4-month period on various concentrations of pseudoephedrine HCl dissolved in D2O (0.0610 to 93.60 mg/mL) containing maleic acid (the internal standard) to yield signal-to-noise ratios ranging from 3 to 72,000 for analyte integral regions. The resulting 5436 purities exhibited a normal distribution about the best estimate of the true value. The median absolute deviation (MAD) statistical method was used to obtain a model of uncertainty relative to the signal-to-noise of the analyte's integral peaks. The model was then tested using different concentrations of known purity chloroquine diphosphate. qNMR results of numerous illicit heroin HCl samples were compared to those obtained by capillary electrophoresis. PMID:25273593

  13. Protein structure determination by combining sparse NMR data with evolutionary couplings

    PubMed Central

    Tang, Yuefeng; Huang, Yuanpeng Janet; Hopf, Thomas A.; Sander, Chris; Marks, Debora S.; Montelione, Gaetano T.

    2015-01-01

    Accurate protein structure determination by NMR is challenging for larger proteins, for which experimental data is often incomplete and ambiguous. Fortunately, the upsurge in evolutionary sequence information and advances in maximum entropy statistical methods now provide a rich complementary source of structural constraints. We have developed a hybrid approach (EC-NMR) combining sparse NMR data with evolutionary residue-residue couplings, and demonstrate accurate structure determination for several 6 to 41 kDa proteins. PMID:26121406

  14. Measurement and assignment of long-range C-H dipolar couplings in liquid crystals by two-dimensional NMR spectroscopy

    SciTech Connect

    Hong, M.; Pines, A. |; Caldarelli, S.

    1996-08-29

    We describe multidimensional NMR techniques to measure and assign {sup 13}C-{sup 1}H dipolar couplings in nematic liquid crystals with high resolution. In particular, dipolar couplings between aromatic and aliphatic sites are extracted, providing valuable information on the structural correlations between these two components of thermotropic liquid crystal molecules. The NMR techniques are demonstrated on 4-pentyl-4`-biphenylcarbonitrile (5CB), a well-characterized room-temperature nematic liquid crystal. Proton-detected local-field NMR spectroscopy is employed to obtain highly resolved C-H dipolar couplings that are separated according to the chemical shifts of the carbon sites. Each {sup 13}C cross section in the 2D spectra exhibits several doublet splittings, with the largest one resulting from the directly bonded C-H coupling. The smaller splittings originate from the long-range C-H dipolar couplings and can be assigned qualitatively by a chemical shift heteronuclear correlation (HETCOR) experiment. The HETCOR experiment incorporates a mixing period for proton spin diffusion to occur, so that maximal polarization transfer can be achieved between the unbonded {sup 13}C and {sup 1}H nuclei. To assign the long-range C-H couplings quantitatively. we combined these two techniques into a novel reduced-3D experiment, in which the {sup 1}H chemical shift-displaced C-H dipolar couplings are correlated with the {sup 13}C chemical shifts. 34 refs., 6 figs., 2 tabs.

  15. Proton-coupled electron transfer in solution, proteins, and electrochemistry.

    PubMed

    Hammes-Schiffer, Sharon; Soudackov, Alexander V

    2008-11-13

    Recent advances in the theoretical treatment of proton-coupled electron transfer (PCET) reactions are reviewed. These reactions play an important role in a wide range of biological processes, as well as in fuel cells, solar cells, chemical sensors, and electrochemical devices. A unified theoretical framework has been developed to describe both sequential and concerted PCET, as well as hydrogen atom transfer (HAT). A quantitative diagnostic has been proposed to differentiate between HAT and PCET in terms of the degree of electronic nonadiabaticity, where HAT corresponds to electronically adiabatic proton transfer and PCET corresponds to electronically nonadiabatic proton transfer. In both cases, the overall reaction is typically vibronically nonadiabatic. A series of rate constant expressions have been derived in various limits by describing the PCET reactions in terms of nonadiabatic transitions between electron-proton vibronic states. These expressions account for the solvent response to both electron and proton transfer and the effects of the proton donor-acceptor vibrational motion. The solvent and protein environment can be represented by a dielectric continuum or described with explicit molecular dynamics. These theoretical treatments have been applied to numerous PCET reactions in solution and proteins. Expressions for heterogeneous rate constants and current densities for electrochemical PCET have also been derived and applied to model systems. PMID:18842015

  16. Exchangers man the pumps: Functional interplay between proton pumps and proton-coupled Ca(2+) exchangers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tonoplast-localised proton-coupled Ca(2+) transporters encoded by cation/H(+) exchanger (CAX) genes play a critical role in sequestering Ca(2+) into the vacuole. These transporters may function in coordination with Ca(2+) release channels, to shape stimulus-induced cytosolic Ca(2+) elevations. Recen...

  17. Proton and nitrogen-15 NMR spectroscopic studies of hydrogen ion-dependent pseudo-halide ion binding to chloroperoxidase

    SciTech Connect

    Lukat, G.S.; Goff, H.M.

    1986-12-15

    The proton nuclear magnetic resonance spectra of several chloroperoxidase-inhibitor complexes have been investigated. Titrations of chloroperoxidase with azide, thiocyanate, cyanate, or nitrite ions indicate that only the chloroperoxidase-thiocyanate complex exhibits slow ligand exchange on the 360-MHz NMR time scale. The temperature dependence of the proton NMR spectra of the complexes suggests that, although the complexes are predominantly low-spin ferric heme iron, a spin equilibrium is present presumably between S = 1/2 and S = 5/2 states. The pH dependence of the proton NMR spectra of the psuedo-halide-chloroperoxidase complexes was examined at 360 and 90 MHz. Chloroperoxidase complexes with azide and cyanate show similar behavior; 360-MHz proton spectra are readily observed at low pH (less than 5.0) but not at high pH. At high pH, the ligand exchange rate falls in an intermediate time range. When the complexes are examined at 90 MHz, however, spectra consisting of averaged signals are observed. The chloroperoxidase-thiocyanate complex does not form at high pH values; the proton NMR spectrum observed is that of native chloroperoxidase. The pKa for the chloroperoxidase-thiocyanate heme-linked ionizable amino acid residue falls between 4.2 and 5.0. Only an averaged azide signal was observed in the nitrogen-15 NMR spectra for solutions that contained the azide complex of chloroperoxidase, horseradish peroxidase, and myoglobin.

  18. Proton and nitrogen-15 NMR spectroscopic studies of hydrogen ion-dependent pseudo-halide ion binding to chloroperoxidase.

    PubMed

    Lukat, G S; Goff, H M

    1986-12-15

    The proton nuclear magnetic resonance spectra of several chloroperoxidase-inhibitor complexes have been investigated. Titrations of chloroperoxidase with azide, thiocyanate, cyanate, or nitrite ions indicate that only the chloroperoxidase-thiocyanate complex exhibits slow ligand exchange on the 360-MHz NMR time scale. The temperature dependence of the proton NMR spectra of the complexes suggests that, although the complexes are predominantly low-spin ferric heme iron, a spin equilibrium is present presumably between S = 1/2 and S = 5/2 states. The pH dependence of the proton NMR spectra of the psuedo-halide-chloroperoxidase complexes was examined at 360 and 90 MHz. Chloroperoxidase complexes with azide and cyanate show similar behavior; 360-MHz proton spectra are readily observed at low pH (less than 5.0) but not at high pH. At high pH, the ligand exchange rate falls in an intermediate time range. When the complexes are examined at 90 MHz, however, spectra consisting of averaged signals are observed. The chloroperoxidase-thiocyanate complex does not form at high pH values; the proton NMR spectrum observed is that of native chloroperoxidase. The pKa for the chloroperoxidase-thiocyanate heme-linked ionizable amino acid residue falls between 4.2 and 5.0. Only an averaged azide signal was observed in the nitrogen-15 NMR spectra for solutions that contained the azide complex of chloroperoxidase, horseradish peroxidase, and myoglobin. PMID:3023353

  19. Residual methyl protonation in perdeuterated proteins for multi-dimensional correlation experiments in MAS solid-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Agarwal, Vipin; Reif, Bernd

    2008-09-01

    NMR studies involving perdeuterated proteins focus in general on exchangeable amide protons. However, non-exchangeable sites contain as well a small amount of protons as the employed precursors for protein biosynthesis are not completely proton depleted. The degree of methyl group protonation is in the order of 9% for CD 2H using >97% deuterium enriched glucose. We show in this manuscript that this small amount of residual protonation is sufficient to perform 2D and 3D MAS solid-state NMR experiments. In particular, we suggest a HCCH-TOBSY type experiment which we successfully employ to assign the methyl resonances in aliphatic side chains in a perdeuterated sample of the SH3 domain of chicken α-spectrin.

  20. 1H NMR studies of maltose, maltoheptaose, alpha-, beta-, and gamma-cyclodextrins, and complexes in aqueous solutions with hydroxy protons as structural probes.

    PubMed

    Bekiroglu, Somer; Kenne, Lennart; Sandström, Corine

    2003-03-01

    The (1)H NMR chemical shifts, coupling constants, temperature coefficients, and exchange rates have been measured for the hydroxy protons of aqueous solutions of alpha-, beta-, and gamma-cyclodextrins, maltose, and maltoheptaose. In cyclodextrins (CDs), the high chemical shift of the O(3)H signal and its small (3)J(OH,CH) value suggest that O(3)H is involved in a hydrogen bond. The small temperature coefficients and rate of exchange values of O(2)H and O(3)H confirm the involvement of O(3)H in hydrogen bonding and indicate that O(2)H is the hydrogen bond partner. In maltose, two distinct NMR signals with two different vicinal coupling constants are found for O(2')H. A cross-peak in the ROESY spectrum indicates chemical exchange between the O(2')H and O(3)H protons. The existence of two distinct NMR signals with different J values for O(2')H shows the influence of anomeric configuration on the O(2')H-O(3)H interaction. The effect of complexation with methyl benzoate, adamantane-1-carboxylic acid, adamantane-1-ol, and l- and d-tryptophane on the NMR spectra of the hydroxy protons of alpha-, beta-, and gamma-cyclodextrins and of maltose has been investigated. No significant spectral changes were observed upon addition of methyl benzoate and adamantane-1-carboxylic acid. The addition of adamantane-1-ol resulted in an upfield shift and a strong broadening of the O(2)H signal from alpha-CD, and a small temperature coefficient was measured upon complexation. The O(2)H and O(3)H signals in beta-CD were broadened and shifted downfield upon addition of l- and d-tryptophane. PMID:12608778

  1. Symmetrization of cationic hydrogen bridges of protonated sponges induced by solvent and counteranion interactions as revealed by NMR spectroscopy.

    PubMed

    Pietrzak, Mariusz; Wehling, Jens P; Kong, Shushu; Tolstoy, Peter M; Shenderovich, Ilya G; López, Concepción; Claramunt, Rosa María; Elguero, José; Denisov, Gleb S; Limbach, Hans-Heinrich

    2010-02-01

    The properties of the intramolecular hydrogen bonds of doubly (15)N-labeled protonated sponges of the 1,8-bis(dimethylamino)naphthalene (DMANH(+)) type have been studied as a function of the solvent, counteranion, and temperature using low-temperature NMR spectroscopy. Information about the hydrogen-bond symmetries was obtained by the analysis of the chemical shifts delta(H) and delta(N) and the scalar coupling constants J(N,N), J(N,H), J(H,N) of the (15)NH(15)N hydrogen bonds. Whereas the individual couplings J(N,H) and J(H,N) were averaged by a fast intramolecular proton tautomerism between two forms, it is shown that the sum |J(N,H)+J(H,N)| generally represents a measure of the hydrogen-bond strength in a similar way to delta(H) and J(N,N). The NMR spectroscopic parameters of DMANH(+) and of 4-nitro-DMANH(+) are independent of the anion in the case of CD(3)CN, which indicates ion-pair dissociation in this solvent. By contrast, studies using CD(2)Cl(2), [D(8)]toluene as well as the freon mixture CDF(3)/CDF(2)Cl, which is liquid down to 100 K, revealed an influence of temperature and of the counteranions. Whereas a small counteranion such as trifluoroacetate perturbed the hydrogen bond, the large noncoordinating anion tetrakis[3,5-bis(trifluoromethyl)phenyl]borate B[{C(6)H(3)(CF(3))(2)}(4)](-) (BARF(-)), which exhibits a delocalized charge, made the hydrogen bond more symmetric. Lowering the temperature led to a similar symmetrization, an effect that is discussed in terms of solvent ordering at low temperature and differential solvent order/disorder at high temperatures. By contrast, toluene molecules that are ordered around the cation led to typical high-field shifts of the hydrogen-bonded proton as well as of those bound to carbon, an effect that is absent in the case of neutral NHN chelates. PMID:20024986

  2. Protonation and Proton-Coupled Electron Transfer at S-Ligated [4Fe-4S] Clusters.

    PubMed

    Saouma, Caroline T; Morris, Wesley D; Darcy, Julia W; Mayer, James M

    2015-06-15

    Biological [Fe-S] clusters are increasingly recognized to undergo proton-coupled electron transfer (PCET), but the site of protonation, mechanism, and role for PCET remains largely unknown. Here we explore this reactivity with synthetic model clusters. Protonation of the arylthiolate-ligated [4Fe-4S] cluster [Fe4 S4 (SAr)4 ](2-) (1, SAr=S-2,4-6-(iPr)3 C6 H2 ) leads to thiol dissociation, reversibly forming [Fe4 S4 (SAr)3 L](1-) (2) and ArSH (L=solvent, and/or conjugate base). Solutions of 2+ArSH react with the nitroxyl radical TEMPO to give [Fe4 S4 (SAr)4 ](1-) (1ox ) and TEMPOH. This reaction involves PCET coupled to thiolate association and may proceed via the unobserved protonated cluster [Fe4 S4 (SAr)3 (HSAr)](1-) (1-H). Similar reactions with this and related clusters proceed comparably. An understanding of the PCET thermochemistry of this cluster system has been developed, encompassing three different redox levels and two protonation states. PMID:25965413

  3. Protonation and Proton-Coupled Electron Transfer at S-Ligated [4Fe-4S] Clusters

    PubMed Central

    Morris, Wesley D.; Darcy, Julia W.; Mayer, James M.

    2015-01-01

    Biological [Fe-S] clusters are increasingly recognized to undergo proton-coupled electron transfer (PCET), but the site of protonation, mechanism, and role for PCET remains largely unknown. Here we explore this reactivity with synthetic model clusters. Protonation of the arylthiolate-ligated [4Fe-4S] cluster [Fe4S4(SAr)4]2- (1, SAr = S-2,4-6-(iPr)3C6H2) leads to thiol dissociation, reversibly forming [Fe4S4(SAr)3L]1- (2) + ArSH (L = solvent, and/or conjugate base). Solutions of 2 + ArSH react with the nitroxyl radical TEMPO to give [Fe4S4(SAr)4]1- (1ox) and TEMPOH. This reaction involves PCET coupled to thiolate association and may proceed via the unobserved protonated cluster [Fe4S4(SAr)3(HSAr)]1-(1-H). Similar reactions with this and related clusters proceed comparably. An understanding of the PCET thermochemistry of this cluster system has been developed, encompassing three different redox levels and two protonation states. PMID:25965413

  4. ¹H and (15)N NMR Analyses on Heparin, Heparan Sulfates and Related Monosaccharides Concerning the Chemical Exchange Regime of the N-Sulfo-Glucosamine Sulfamate Proton.

    PubMed

    Pomin, Vitor H

    2016-01-01

    Heparin and heparan sulfate are structurally related glycosaminoglycans (GAGs). Both GAGs present, although in different concentrations, N-sulfo-glucosamine (GlcNS) as one of their various composing units. The conditional fast exchange property of the GlcNS sulfamate proton in these GAGs has been pointed as the main barrier to its signal detection via NMR experiments, especially ¹H-(15)N HSQC. Here, a series of NMR spectra is collected on heparin, heparan sulfate and related monosaccharides. The N-acetyl glucosamine-linked uronic acid types of these GAGs were properly assigned in the ¹H-(15)N HSQC spectra. Dynamic nuclear polarization (DNP) was employed in order to facilitate 1D spectral acquisition of the sulfamate (15)N signal of free GlcNS. Analyses on the multiplet pattern of scalar couplings of GlcNS (15)N has helped to understand the chemical properties of the sulfamate proton in solution. The singlet peak observed for GlcNS happens due to fast chemical exchange of the GlcNS sulfamate proton in solution. Analyses on kinetics of alpha-beta anomeric mutarotation via ¹H NMR spectra have been performed in GlcNS as well as other glucose-based monosaccharides. 1D ¹H and 2D ¹H-(15)N HSQC spectra recorded at low temperature for free GlcNS dissolved in a proton-rich solution showed signals from all exchangeable protons, including those belonging to the sulfamate group. This work suits well to the current grand celebration of one-century-anniversary of the discovery of heparin. PMID:27618066

  5. Low Temperature 1H MAS NMR Spectroscopy Studies of Proton Motion in Zeolite

    SciTech Connect

    Huo, H.; Peng, L; Grey, C

    2009-01-01

    Low temperature {sup 1}H MAS NMR spectroscopy is used to study protonic motion in zeolite HZSM-5 in both samples that have been dried using procedures that are standard in the literature and samples that have been more carefully dehydrated. A significant enhancement of proton mobility is seen for the ''standard'' dehydrated HZSM-5 sample in comparison to that seen for the much drier sample. This is ascribed to a vehicle-hopping mechanism involving the residual water that is present in these zeolites. A gradual change of the framework structure is observed on cooling to approximately 213 K, as monitored via the change in {sup 1}H chemical shift values of the Broensted acid resonances and by X-ray diffraction. A more sudden change in structure is seen by differential scanning calorimetry and NMR at approximately 220?230 K, which is associated with changes in both the mobility and the modes of binding of the residual water to the Broensted acid sites and the zeolite framework.

  6. 1H NMR study of proton dynamics in the inorganic solid acid Rb3 H( SO4 )2

    NASA Astrophysics Data System (ADS)

    Suzuki, Koh-Ichi; Hayashi, Shigenobu

    2006-01-01

    Proton dynamics in Rb3H(SO4)2 has been studied by means of H1 NMR. The H1 magic-angle-spinning (MAS) NMR spectra were traced at room temperature (RT) at Larmor frequency of 400.13MHz . H1 static NMR spectra were measured at frequencies of 200.13MHz and 400.13MHz in the ranges of 165-513 and 300-513K , respectively. H1 spin-lattice relaxation times, T1 , were measured at 200.13 and 19.65MHz in the ranges of 260-513 and 260-470K , respectively. The H1 MAS NMR spectrum at 294K has an isotropic chemical shift of 16.3ppm from tetramethylsilane, demonstrating very strong hydrogen bonds. In RT phase, a wobbling motion of the O-H axis in one direction at the fast motional limit takes place above 400K , being supported by the H1 static NMR spectral line shapes and by the H1 T1 values. In the high temperature (HT) phase, the sharp H1 static NMR spectra indicate translational proton diffusion. From the analysis of H1 T1 , protons diffuse with the inverse of the frequency factor (τ0) of 9.5×10-13s and the activation energy (Ea) of 25kJmol-1 . These parameters can well explain the macroscopic electric conductivity in HT phase.

  7. Nanoantioxidant-driven plasmon enhanced proton-coupled electron transfer

    NASA Astrophysics Data System (ADS)

    Sotiriou, Georgios A.; Blattmann, Christoph O.; Deligiannakis, Yiannis

    2015-12-01

    Proton-coupled electron transfer (PCET) reactions involve the transfer of a proton and an electron and play an important role in a number of chemical and biological processes. Here, we describe a novel phenomenon, plasmon-enhanced PCET, which is manifested using SiO2-coated Ag nanoparticles functionalized with gallic acid (GA), a natural antioxidant molecule that can perform PCET. These GA-functionalized nanoparticles show enhanced plasmonic response at near-IR wavelengths, due to particle agglomeration caused by the GA molecules. Near-IR laser irradiation induces strong local hot-spots on the SiO2-coated Ag nanoparticles, as evidenced by surface enhanced Raman scattering (SERS). This leads to plasmon energy transfer to the grafted GA molecules that lowers the GA-OH bond dissociation enthalpy by at least 2 kcal mol-1 and therefore facilitates PCET. The nanoparticle-driven plasmon-enhancement of PCET brings together the so far unrelated research domains of nanoplasmonics and electron/proton translocation with significant impact on applications based on interfacial electron/proton transfer.Proton-coupled electron transfer (PCET) reactions involve the transfer of a proton and an electron and play an important role in a number of chemical and biological processes. Here, we describe a novel phenomenon, plasmon-enhanced PCET, which is manifested using SiO2-coated Ag nanoparticles functionalized with gallic acid (GA), a natural antioxidant molecule that can perform PCET. These GA-functionalized nanoparticles show enhanced plasmonic response at near-IR wavelengths, due to particle agglomeration caused by the GA molecules. Near-IR laser irradiation induces strong local hot-spots on the SiO2-coated Ag nanoparticles, as evidenced by surface enhanced Raman scattering (SERS). This leads to plasmon energy transfer to the grafted GA molecules that lowers the GA-OH bond dissociation enthalpy by at least 2 kcal mol-1 and therefore facilitates PCET. The nanoparticle-driven plasmon

  8. Transverse beam coupling impedance of the CERN Proton Synchrotron

    NASA Astrophysics Data System (ADS)

    Persichelli, S.; Migliorati, M.; Biancacci, N.; Gilardoni, S.; Metral, E.; Salvant, B.

    2016-04-01

    Beam coupling impedance is a fundamental parameter to characterize the electromagnetic interaction of a particle beam with the surrounding environment. Synchrotron machine performances are critically affected by instabilities and collective effects triggered by beam coupling impedance. In particular, transverse beam coupling impedance is expected to impact beam dynamics of the CERN Proton Synchrotron (PS), since a significant increase in beam intensity is foreseen within the framework of the LHC Injectors Upgrade (LIU) project. In this paper we describe the study of the transverse beam coupling impedance of the PS, taking into account the main sources of geometrical impedance and the contribution of indirect space charge at different energies. The total machine impedance budget, determined from beam-based dedicated machine measurement sessions, is also discussed and compared with the theoretical model.

  9. Integrating proton coupled electron transfer (PCET) and excited states

    SciTech Connect

    Gagliardi, Christopher J.; Westlake, Brittany C.; Kent, Caleb A.; Paul, Jared J.; Papanikolas, John M.; Meyer, Thomas J.

    2010-11-01

    In many of the chemical steps in photosynthesis and artificial photosynthesis, proton coupled electron transfer (PCET) plays an essential role. An important issue is how excited state reactivity can be integrated with PCET to carry out solar fuel reactions such as water splitting into hydrogen and oxygen or water reduction of CO2 to methanol or hydrocarbons. The principles behind PCET and concerted electron–proton transfer (EPT) pathways are reasonably well understood. In Photosystem II antenna light absorption is followed by sensitization of chlorophyll P680 and electron transfer quenching to give P680+. The oxidized chlorophyll activates the oxygen evolving complex (OEC), a CaMn4 cluster, through an intervening tyrosine–histidine pair, YZ. EPT plays a major role in a series of four activation steps that ultimately result in loss of 4e-/4H+ from the OEC with oxygen evolution. The key elements in photosynthesis and artificial photosynthesis – light absorption, excited state energy and electron transfer, electron transfer activation of multiple-electron, multiple-proton catalysis – can also be assembled in dye sensitized photoelectrochemical synthesis cells (DS-PEC). In this approach, molecular or nanoscale assemblies are incorporated at separate electrodes for coupled, light driven oxidation and reduction. Separate excited state electron transfer followed by proton transfer can be combined in single semi-concerted steps (photo-EPT) by photolysis of organic charge transfer excited states with H-bonded bases or in metal-to-ligand charge transfer (MLCT) excited states in pre-associated assemblies with H-bonded electron transfer donors or acceptors. In these assemblies, photochemically induced electron and proton transfer occur in a single, semi-concerted event to give high-energy, redox active intermediates.

  10. Surface NMR measurement of proton relaxation times in medium to coarse-grained sand aquifer.

    PubMed

    Shushakov, O A

    1996-01-01

    A surface NMR investigation of groundwater in the geomagnetic field is under study. To detect the surface NMR a wire loop with a diameter of about 100 m, being an antenna for both an exciting field source and the NMR signal receiver, is laid out on the ground. A sinusoidal current pulse with a rectangular envelope is passed through the loop to excite the NMR signal. The carrier frequency of the oscillating current in this pulse is equal to the Larmor frequency of protons in the Earth's magnetic field. The current amplitude is changed up to 200 amps and the pulse duration is fixed and is equal to 40 ms. The exciting pulse is followed by an induction emf signal caused by the Larmor nuclear precession in geomagnetic field. The relaxation times T1, T2, and T2* were measured by the surface NMR for both groundwater in medium to coarse-grained sand at borehole and for bulk water under the ice surface of frozen lake. To determine T1, a longitudinal interference in experiments with repeated pulses was measured. A sequence with equal period between equal excitation pulses was used. The relaxation times T1, T2, measured for bulk water under the ice of the Ob reservoir were 1.0 s and 0.7 s, respectively. To estimate an influence of dissolved oxygen T1 of the same water at the same temperature was measured by lab NMR with and without pumping of oxygen. The relaxation time T1 measured for water in the medium to coarse-grained sand is 0.65 s. The relaxation time T2 estimated by spin echo sequence is found to be equal to 0.15 s. The relaxation time T2* is found to be about 80 ms. This result contradicts published earlier phenomenological correlation between relaxation time T2* and grain size of water-bearing rock. This could be as a result of unsound approach based on grain size or influence of paramagnetic impurities. PMID:8970122

  11. Analysis of the carbon-13 and proton NMR spectra of bovine chromaffin granules.

    PubMed

    Sharp, R R; Richards, E P

    1977-03-29

    Natural abundance carbon-13 and proton NMR spectra of bovine chromaffin granules have been obtained and analyzed using computer simulation techniques. High resolution spectra show the presence of a fluid aqueous phase containing epinephrine, ATP and a random coil protein. The protein spectrum contains unusually intense resonances due to glutamic acid and proline and has been simulated satisfactorily using the known amino acid composition of chromogranin A. The lipid phase of chromaffin granules gives rise to intense, but very broad, resonances in the carbon-13 spectrum. Protons in the lipid phase are also observable as a very rapid component of the proton-free induction decay (T2 approximately equal to 15 microns). Linewidths of the carbon-13 spectra have been used to set upper limits on rotational correlation times and on the motional anisotropy in the aqueous phase. These limits show that the aqueous phase is a simple solution (not a gel) that is isotropic over regions much larger than solute dimensions. No gel transition is observed between -3 and 25 degrees C. The carbon-13 spectra are definitely inconsistent with a lipoprotein matrix model and chromaffin granules previously proposed by Helle and Serck-Hanssen ((1975) Mol. Cell, Biochem. 6, 127-146). Relative carbon-13 intensities of ATP and epinephrine are not consistent with the known 1 : 4 mol ratio of these components. This fact suggests that epinephrine and ATP are not directly complexed in intact chromaffin granules. PMID:849474

  12. Proton-Detected 2D Radio Frequency Driven Recoupling Solid-state NMR Studies on Micelle-associated Cytochrome-b5

    PubMed Central

    Pandey, Manoj Kumar; Vivekanandan, Subramanian; Yamamoto, Kazutoshi; Im, Sangchoul; Waskell, Lucy; Ramamoorthy, Ayyalusamy

    2014-01-01

    Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled (13C, 15N and 2H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged 1H-1H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross peak intensities against the mixing time - obtained from 2D 1H-1H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) - can provide insights into protein dynamics and could be useful to measure 1H-1H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent 1H-1H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from 1H-1H RFDR experiments. The appearance of resonances with distinct chemical shift values in 1H-1H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles. PMID:24657390

  13. Proton-detected 2D radio frequency driven recoupling solid-state NMR studies on micelle-associated cytochrome-b5

    NASA Astrophysics Data System (ADS)

    Pandey, Manoj Kumar; Vivekanandan, Subramanian; Yamamoto, Kazutoshi; Im, Sangchoul; Waskell, Lucy; Ramamoorthy, Ayyalusamy

    2014-05-01

    Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled (13C, 15N and 2H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged 1H-1H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross-peak intensities against the mixing time - obtained from 2D 1H-1H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) - can provide insights into protein dynamics and could be useful to measure 1H-1H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent 1H-1H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from 1H-1H RFDR experiments. The appearance of resonances with distinct chemical shift values in 1H-1H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles.

  14. New approach for characterization of gelatin biopolymer films using proton behavior determined by low field 1H NMR spectrometry.

    PubMed

    Kim, Young-Teck; Hong, Young-Shick; Kimmel, Robert M; Rho, Jeong-Hae; Lee, Cherl-Ho

    2007-12-26

    The behavior of protons in biopolymer films (BFs) formed with gelatin, water, and glycerol was investigated at various relative humidities (RHs) and concentrations of glycerol using a low field 1H NMR spectrometer. At a RH of approximately 0%, the distributed spin-spin relaxation times (T2) of protons in BFs showed two components: a rapidly relaxing proton with the shortest T2 derived from protons in the rigid backbone of the gelatin polymer such as CH1-, CH2-, and CH3-, and a slowly relaxing component with longer T2 from protons of the functional groups in amino acid residues in gelatin such as -OH, -COOH, and -NH3. These two components are referred to as nonexchangeable (T2N) and exchangeable protons (T2E), respectively, indicating the different mobility of the protons. The T2E increased as RH increased indicating the increase in relative mobility of protons due to the larger free volume in the BF matrix. Above a RH of 33%, the slowest relaxing component was found in all BFs and referred to as hydration-water protons (T2W) with the highest relative mobility of all protons in the films. It suggests that the free volume in BFs can be formed above a RH of 33% in the absence of glycerol. The behaviors of T2N, T2E, and T2W reveal the formation of free volume in the BF matrix associated with the presence of plasticizers (water and glycerol). The T2 behavior in BFs is consistent with the behavior of spin-lattice relaxation (T1). Our result is the first attempt to characterize using low field 1H NMR technology how all protons in a film matrix behave and to develop correlations between proton mobility and free volume in protein-based BFs plasticized with water and glycerol. PMID:18052122

  15. Nanoantioxidant-driven plasmon enhanced proton-coupled electron transfer.

    PubMed

    Sotiriou, Georgios A; Blattmann, Christoph O; Deligiannakis, Yiannis

    2016-01-14

    Proton-coupled electron transfer (PCET) reactions involve the transfer of a proton and an electron and play an important role in a number of chemical and biological processes. Here, we describe a novel phenomenon, plasmon-enhanced PCET, which is manifested using SiO2-coated Ag nanoparticles functionalized with gallic acid (GA), a natural antioxidant molecule that can perform PCET. These GA-functionalized nanoparticles show enhanced plasmonic response at near-IR wavelengths, due to particle agglomeration caused by the GA molecules. Near-IR laser irradiation induces strong local hot-spots on the SiO2-coated Ag nanoparticles, as evidenced by surface enhanced Raman scattering (SERS). This leads to plasmon energy transfer to the grafted GA molecules that lowers the GA-OH bond dissociation enthalpy by at least 2 kcal mol(-1) and therefore facilitates PCET. The nanoparticle-driven plasmon-enhancement of PCET brings together the so far unrelated research domains of nanoplasmonics and electron/proton translocation with significant impact on applications based on interfacial electron/proton transfer. PMID:26505730

  16. Analyzing and Interpreting NMR Spin-Spin Coupling Constants Using Molecular Orbital Calculations

    ERIC Educational Resources Information Center

    Autschbach, Jochen; Le Guennic, Boris

    2007-01-01

    Molecular orbital plots are used to analyze and interpret NMR spin-spin coupling constants, also known as J coupling constants. Students have accepted the concept of contributions to molecular properties from individual orbitals without the requirement to provide explicit equations.

  17. Proton transfer and energy coupling in the bacteriorhodopsin photocycle

    NASA Technical Reports Server (NTRS)

    Lanyi, J. K.

    1992-01-01

    A description of the rate constants and the energetics of the elementary reaction steps of the photocycle of bacteriorhodopsin has been helpful in understanding the mechanism of proton transport in this light-driven pump. The evidence suggests a single unbranched reaction sequence, BR-hv----K in equilibrium with L in equilibrium with M1----M2 in equilibrium with N in equilibrium with O----BR, where coupling to the proton-motive force is at the energetically and mechanistically important M1----M2 step. The consequences of site-specific mutations expressed homologously in Halobacterium halobium have revealed characteristics of the Schiff base deprotonation in the L----M1 reaction, the reorientation of the Schiff base from the extracellular to the cytoplasmic side in the M1----M2 reaction, and the reprotonation of the Schiff base in the M2----N reaction.

  18. Catalytic Olefin Hydroamidation Enabled by Proton-Coupled Electron Transfer

    PubMed Central

    2015-01-01

    Here we report a ternary catalyst system for the intramolecular hydroamidation of unactivated olefins using simple N-aryl amide derivatives. Amide activation in these reactions occurs via concerted proton-coupled electron transfer (PCET) mediated by an excited state iridium complex and weak phosphate base to furnish a reactive amidyl radical that readily adds to pendant alkenes. A series of H-atom, electron, and proton transfer events with a thiophenol cocatalyst furnish the product and regenerate the active forms of the photocatalyst and base. Mechanistic studies indicate that the amide substrate can be selectively homolyzed via PCET in the presence of the thiophenol, despite a large difference in bond dissociation free energies between these functional groups. PMID:26439818

  19. In vitro proton NMR study of collagen in human aortic wall.

    PubMed

    Vinée, P; Meurer, B; Constantinesco, A; Kohlberger, B; Hauenstein, K H; Laubenberger, J

    1993-03-01

    The authors relate the findings in the 1H solid state line shape (at 60 MHz) of human aortic walls (n = 12) in native state and after histologically controlled selective lysis of collagen and elastin. An analysis of the line shape shows a composite free induction decay (FID) consisting of a low amplitude (3-7%) fast decaying component (T2 approximately 20 microseconds) and a slow decaying one (T2 > 1 ms). The fast component is identified as the protons of the collagen macromolecules. The second moment computed from the experimental fast component of the FID is in agreement with published studies examining the motional characteristics of collagen by multinuclear NMR employing spin labeling. A theoretical second moment is computed for the collagen macromolecular backbone from the atomic positions in the superhelix. Comparison with the observed experimental values allows determination of the step angle (29 degrees) of the fast rotational motion of the collagen strands along their long axis. PMID:8383787

  20. Proton NMR assignments and regular backbone structure of bovine pancreatic ribonuclease A in aqueous solution

    SciTech Connect

    Robertson, A.D. ); Purisima, E.O. Cornell Univ., Ithaca, NY ); Eastman, M.A.; Scheraga, H.A. )

    1989-07-11

    Proton NMR assignments have been made for 121 of the 124 residues of bovine pancreatic ribonuclease A (RNase A). During the first stage of assignment, COSY and relayed COSY data were used to identify 40 amino acid spin systems belonging to alanine, valine, threonine, isoleucine, and serine residues. Approximately 60 other NH-{alpha}CH-{beta}CH systems were also identified but not assigned to specific amino acid type. NOESY data then were used to connect sequentially neighboring spin systems; approximately 475 of the possible 700 resonances in RNase A were assigned in this way. The authors' assignments agree with those for 20 residues assigned previously. NOESY correlations were used to identify regular backbone structure elements in RNase A, which are very similar to those observed in X-ray crystallographic studies.

  1. Proton NMR investigation into the basis for the relatively high redox potential of lignin peroxidase

    SciTech Connect

    Banci, L.; Bertini, I.; Turano, P. ); Ming Tien ); Kirk, T.K. )

    1991-08-15

    Lignin peroxidase shares several structural features with the well-studied horseradish peroxidase and cytochrome c peroxidase but carries a higher redox potential. Here the heme domain of lignin peroxidase and the lignin peroxidase cyanide adduct was examined by {sup 1}H NMR spectroscopy, including nuclear Overhauser effect and two-dimensional measurements, and the findings were compared with those for horseradish peroxidase and cytochrome c peroxidase. Structural information was obtained on the orientation of the heme vinyl and propionate groups and the proximal and distal histidines. The shifts of the {var epsilon}1 proton of the proximal histidine were found to be empirically related to the Fe{sup 3+}/Fe{sup 2+} redox potentials.

  2. Solution NMR Experiment for Measurement of (15)N-(1)H Residual Dipolar Couplings in Large Proteins and Supramolecular Complexes.

    PubMed

    Eletsky, Alexander; Pulavarti, Surya V S R K; Beaumont, Victor; Gollnick, Paul; Szyperski, Thomas

    2015-09-01

    NMR residual dipolar couplings (RDCs) are exquisite probes of protein structure and dynamics. A new solution NMR experiment named 2D SE2 J-TROSY is presented to measure N-H RDCs for proteins and supramolecular complexes in excess of 200 kDa. This enables validation and refinement of their X-ray crystal and solution NMR structures and the characterization of structural and dynamic changes occurring upon complex formation. Accurate N-H RDCs were measured at 750 MHz (1)H resonance frequency for 11-mer 93 kDa (2)H,(15)N-labeled Trp RNA-binding attenuator protein tumbling with a correlation time τc of 120 ns. This is about twice as long as that for the most slowly tumbling system, for which N-H RDCs could be measured, so far, and corresponds to molecular weights of ∼200 kDa at 25 °C. Furthermore, due to the robustness of SE2 J-TROSY with respect to residual (1)H density from exchangeable protons, increased sensitivity at (1)H resonance frequencies around 1 GHz promises to enable N-H RDC measurement for even larger systems. PMID:26293598

  3. Collection of NMR Scalar and Residual Dipolar Couplings Using a Single Experiment.

    PubMed

    Gil-Silva, Leandro F; Santamaría-Fernández, Raquel; Navarro-Vázquez, Armando; Gil, Roberto R

    2016-01-11

    A new DMSO-compatible aligning gel based on cross-linked poly(2-hydroxylethyl methacrylate) (poly-HEMA) has been developed. Due to a significant difference in bulk magnetic susceptibility between the DMSO inside and outside the gel, it is possible to simultaneously collect isotropic and anisotropic NMR data, such as residual dipolar couplings (RDC), in the same NMR tube. RDC-assisted structural analysis of menthol and the alkaloid retrorsine is reported as proof of concept. PMID:26515991

  4. Search for a coupling of the proton spin to gravity

    NASA Astrophysics Data System (ADS)

    Jackson Kimball, Derek; Dudley, Jordan; Li, Yan; Patel, Dilan

    2016-05-01

    We present an overview of progress in our search for a long-range coupling between rubidium (Rb) nuclear spins and the mass of the Earth, which can be interpreted as a search for a long-range monopole-dipole interaction or a spin-gravity coupling. The experiment consists of simultaneous measurement of the spin precession frequencies of overlapping ensembles of Rb-85 and Rb-87 atoms contained within an evacuated, antirelaxation-coated vapor cell. Because of the nuclear structure of Rb-85 and Rb-87, the experiment is particularly sensitive to anomalous spin-dependent interactions of the proton. We have studied a number of important systematic effects related to vector and tensor light shifts, optical pumping effects, the ac and nonlinear Zeeman effects, and magnetic field gradients. We anticipate that our experiment can improve sensitivity to anomalous long-range spin-mass couplings of the proton compared to previous experiments by more than an order of magnitude. Supported by the National Science Foundation under Grant PHY-1307507.

  5. Helical stacking in DNA three-way junctions containing two unpaired pyrimidines: proton NMR studies.

    PubMed Central

    Leontis, N B; Hills, M T; Piotto, M; Ouporov, I V; Malhotra, A; Gorenstein, D G

    1995-01-01

    The proton NMR spectra of DNA three-way junction complexes (TWJ) having unpaired pyrimidines, 5'-TT- and 5'-TC- on one strand at the junction site were assigned from 2D NOESY spectra acquired in H2O and D2O solvents and homonuclear 3D NOESY-TOCSY and 3D NOESY-NOESY in D2O solvent. TWJ are the simplest branched structures found in biologically active nucleic acids. Unpaired nucleotides are common features of such structures and have been shown to stabilize junction formation. The NMR data confirm that the component oligonucleotides assemble to form conformationally homogeneous TWJ complexes having three double-helical, B-form arms. Two of the helical arms stack upon each other. The unpaired pyrimidine bases lie in the minor groove of one of the helices and are partly exposed to solvent. The coaxial stacking arrangement deduced is different from that determined by Rosen and Patel (Rosen, M.A., and D.J. Patel. 1993. Biochemistry. 32:6576-6587) for a DNA three-way junction having two unpaired cytosines, but identical to that suggested by Welch et al. (Welch, J. B., D. R. Duckett, D. M. J. Lilley. 1993. Nucleic Acids Res. 21:4548-4555) on the basis of gel electrophoretic studies of DNA three-way junctions containing unpaired adenosines and thymidines. Images FIGURE 2 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 PMID:7711249

  6. Resolving intermediates in biological proton-coupled electron transfer: A tyrosyl radical prior to proton movement

    PubMed Central

    Faller, Peter; Goussias, Charilaos; Rutherford, A. William; Un, Sun

    2003-01-01

    The coupling of proton chemistry with redox reactions is important in many enzymes and is central to energy transduction in biology. However, the mechanistic details are poorly understood. Here, we have studied tyrosine oxidation, a reaction in which the removal of one electron from the amino acid is linked to the release of its phenolic proton. Using the unique photochemical properties of photosystem II, it was possible to oxidize the tyrosine at 1.8 K, a temperature at which proton and protein motions are limited. The state formed was detected by high magnetic field EPR as a high-energy radical intermediate trapped in an unprecedentedly electropositive environment. Warming of the protein allows this state to convert to a relaxed, stable form of the radical. The relaxation event occurs at 77 K and seems to involve proton migration and only a very limited movement of the protein. These reactions represent a stabilization process that prevents the back-reaction and determines the reactivity of the radical. PMID:12855767

  7. Resolving intermediates in biological proton-coupled electron transfer: a tyrosyl radical prior to proton movement.

    PubMed

    Faller, Peter; Goussias, Charilaos; Rutherford, A William; Un, Sun

    2003-07-22

    The coupling of proton chemistry with redox reactions is important in many enzymes and is central to energy transduction in biology. However, the mechanistic details are poorly understood. Here, we have studied tyrosine oxidation, a reaction in which the removal of one electron from the amino acid is linked to the release of its phenolic proton. Using the unique photochemical properties of photosystem II, it was possible to oxidize the tyrosine at 1.8 K, a temperature at which proton and protein motions are limited. The state formed was detected by high magnetic field EPR as a high-energy radical intermediate trapped in an unprecedentedly electropositive environment. Warming of the protein allows this state to convert to a relaxed, stable form of the radical. The relaxation event occurs at 77 K and seems to involve proton migration and only a very limited movement of the protein. These reactions represent a stabilization process that prevents the back-reaction and determines the reactivity of the radical. PMID:12855767

  8. The Structural Response of Polyelectrolyte Dendrimer toward the Molecular Protonation: The Inconsistence Revealed by SANS and NMR

    SciTech Connect

    Chen, Wei-Ren; Herwig, Kenneth W; Hong, Kunlun; Li, Xin; Liu, Emily; Liu, Yun; Porcar, L.; Shew, Chwen-Yang; Smith, Gregory Scott; Wu, Bin; Liu, Dazhi; Gao, Carrie Y

    2012-01-01

    Polyamidoamine (PAMAM) dendrimers and their charged state in deuterium oxide have been investigated with diffusion NMR and small angle neutron scattering (SANS) techniques. NMR measurement suggests that, upon increasing the molecular protonation by progressive acidification of solutions, significant variation of hydrodynamic radius, calculated by the Stokes-Einstein relation with given surface condition, is observed upon increasing the molecular protonation. However, comparative SANS experiment indicates little dependence of dendrimer global size, in terms of radius of gyration, on molecular protonation. This observed inconsistence indicates the necessity of incorporating the effect of molecular interface modification by dressed counterion, when dynamical measurements are used for determination the structural characteristics of ionic soft colloids even in a dilute enough suspension.

  9. High-resolution proton CRAMPS NMR using narrowband analog filters and postponed data acquisition

    NASA Astrophysics Data System (ADS)

    Wang, Liying; Zhou, Donghua H.

    2013-09-01

    Proton linewidths decrease with increasing magic-angle spinning (MAS) rates. However, without spin dilution by deuteration, even with the fastest MAS rates available today, the narrowest proton linewidths are obtained by using the combined rotation and multiple pulse spectroscopy (CRAMPS) method. Direct observation under windowed CRAMPS typically introduces several tens of times more noise, partly because wideband analog filters (e.g. 5 MHz) must be used or sometimes even bypassed. Here we report that it is possible to keep using narrowband analog filters (about 50 kHz cutoff frequency) in CRAMPS by taking advantage of the time delay caused by the filters, which is inversely proportional to the cutoff frequency. This delay coincides with typical CRAMPS cycle times, enabling acquisition of the data point in the next detection window. The noise of such CRAMPS spectra is only about 5 times larger than MAS-only spectra. This new method allows CRAMPS to be performed on systems that lack wideline hardware (wideband filters and fast ADCs), for example, older spectrometers originally intended for solution NMR.

  10. Histidine side-chain dynamics and protonation monitored by 13C CPMG NMR relaxation dispersion.

    PubMed

    Hass, Mathias A S; Yilmaz, Ali; Christensen, Hans E M; Led, Jens J

    2009-08-01

    The use of 13C NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically 13C labeled histidine residues in plastocyanin (PCu) from Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for 13C(epsilon1) nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from 15N backbone relaxation measurements. Compared to measurements of backbone nuclei, 13C(epsilon1) dispersion provides a more direct method to monitor interchanging protonation states or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the 13C(epsilon1) dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains are discussed. PMID:19533375

  11. Amide Proton Solvent Protection in Amylin Fibrils Probed by Quenched Hydrogen Exchange NMR

    PubMed Central

    Alexandrescu, Andrei T.

    2013-01-01

    Amylin is an endocrine hormone that accumulates in amyloid plaques in patients with advanced type 2 diabetes. The amyloid plaques have been implicated in the destruction of pancreatic β-cells, which synthesize amylin and insulin. To better characterize the secondary structure of amylin in amyloid fibrils we assigned the NMR spectrum of the unfolded state in 95% DMSO and used a quenched hydrogen-deuterium exchange technique to look at amide proton solvent protection in the fibrils. In this technique, partially exchanged fibrils are dissolved in 95% DMSO and information about amide proton occupancy in the fibrils is determined from DMSO-denatured monomers. Hydrogen exchange lifetimes at pH 7.6 and 37°C vary between ∼5 h for the unstructured N-terminus to 600 h for amide protons in the two β-strands that form inter-molecular hydrogen bonds between amylin monomers along the length of the fibril. Based on the protection data we conclude that residues A8-H18 and I26-Y37 comprise the two β-strands in amylin fibrils. There is variation in protection within the β-strands, particularly for strand β1 where only residues F15-H18 are strongly protected. Differences in protection appear to be due to restrictions on backbone dynamics imposed by the packing of two-layers of C2-symmetry-related β-hairpins in the protofilament structure, with strand β1 positioned on the surface and β2 in the interior. PMID:23457571

  12. Lactonization and protonation of gluconic acid: a thermodynamicand kinetic study by potentiometry, nmr and esi-ms

    SciTech Connect

    Zhang, Z.; Gibson, P.; Clark, S.B.; Tian, G.; Zanonato, P.; Rao, L.

    2007-01-10

    In acidic aqueous solutions, gluconate protonation is coupled with lactonization of gluconic acid. With the decrease of pC{sub H}, two lactones ({delta}/{gamma}) are sequentially formed. The {delta}-lactone forms more readily than the {gamma}-lactone. In 0.1 M gluconate solutions, if pC{sub H} is above 2.5, only the {delta}-lactone is generated. When pC{sub H} is decreased below 2.0, the formation of the {gamma}-lactone is observable although the {delta}-lactone predominates. At I = 0.1 M NaClO{sub 4} and room temperature, the deprotonation constant of the carboxylic group, using the NMR technique, was determined to be log K{sub a} = 3.30 {+-} 0.02; the {delta}-lactonization constant, by the batch potentiometric titrations, was obtained to be log K{sub L} = - (0.54 {+-} 0.04). Using ESI-MS, the rate constants of the {delta}-lactonization and the hydrolysis at pC{sub H} {approx} 5.0 were estimated to be k{sub 1} = 3.2 x 10{sup -5} s{sup -1} and k{sup -1} = 1.1 x 10{sup -4} s{sup -1}, respectively.

  13. On the Importance of Exchangeable NH Protons in Creatine for the Magnetic Coupling of Creatine Methyl Protons in Skeletal Muscle

    NASA Astrophysics Data System (ADS)

    Kruiskamp, M. J.; Nicolay, K.

    2001-03-01

    The methyl protons of creatine in skeletal muscle exhibit a strong off-resonance magnetization transfer effect. The mechanism of this process is unknown. We previously hypothesized that the exchangeable amide/amino protons of creatine might be involved. To test this the characteristics of the creatine magnetization transfer effect were investigated in excised rat hindleg skeletal muscle that was equilibrated in either H2O or D2O solutions containing creatine. The efficiency of off-resonance magnetization transfer to the protons of mobile creatine in excised muscle was similar to that previously reported in intact muscle in vivo. Equilibrating the isolated muscle in D2O solution had no effect on the magnetic coupling to the immobile protons. It is concluded that exchangeable protons play a negligible role in the magnetic coupling of creatine methyl protons in muscle.

  14. Proton-coupled electron transfer with photoexcited metal complexes.

    PubMed

    Wenger, Oliver S

    2013-07-16

    Proton-coupled electron transfer (PCET) plays a crucial role in many enzymatic reactions and is relevant for a variety of processes including water oxidation, nitrogen fixation, and carbon dioxide reduction. Much of the research on PCET has focused on transfers between molecules in their electronic ground states, but increasingly researchers are investigating PCET between photoexcited reactants. This Account describes recent studies of excited-state PCET with d(6) metal complexes emphasizing work performed in my laboratory. Upon photoexcitation, some complexes release an electron and a proton to benzoquinone reaction partners. Others act as combined electron-proton acceptors in the presence of phenols. As a result, we can investigate photoinduced PCET involving electron and proton transfer in a given direction, a process that resembles hydrogen-atom transfer (HAT). In other studies, the photoexcited metal complexes merely serve as electron donors or electron acceptors because the proton donating and accepting sites are located on other parts of the molecular PCET ensemble. We and others have used this multisite design to explore so-called bidirectional PCET which occurs in many enzymes. A central question in all of these studies is whether concerted proton-electron transfer (CPET) can compete kinetically with sequential electron and proton transfer steps. Short laser pulses can trigger excited-state PCET, making it possible to investigate rapid reactions. Luminescence spectroscopy is a convenient tool for monitoring PCET, but unambiguous identification of reaction products can require a combination of luminescence spectroscopy and transient absorption spectroscopy. Nevertheless, in some cases, distinguishing between PCET photoproducts and reaction products formed by simple photoinduced electron transfer (ET) (reactions that don't include proton transfer) is tricky. Some of the studies presented here deal directly with this important problem. In one case study we

  15. Advanced solid-state NMR characterization of marine dissolved organic matter isolated using the coupled reverse osmosis/electrodialysis method.

    PubMed

    Mao, Jingdong; Kong, Xueqian; Schmidt-Rohr, Klaus; Pignatello, Joseph J; Perdue, E Michael

    2012-06-01

    Advanced (13)C solid-state techniques were employed to investigate the major structural characteristics of two surface-seawater dissolved organic matter (DOM) samples isolated using the novel coupled reverse osmosis/electrodialysis method. The NMR techniques included quantitative (13)C direct polarization/magic angle spinning (DP/MAS) and DP/MAS with recoupled dipolar dephasing, (13)C cross-polarization/total sideband suppression (CP/TOSS), (13)C chemical shift anisotropy filter, CH, CH(2), and CH(n) selection, two-dimensional (1)H-(13)C heteronuclear correlation NMR (2D HETCOR), 2D HETCOR combined with dipolar dephasing, and (15)N cross-polarization/magic angle spinning (CP/MAS). The two samples (Coastal and Marine DOM) were collected at the mouth of the Ogeechee River and in the Gulf Stream, respectively. The NMR results indicated that they were structurally distinct. Coastal DOM contained significantly more aromatic and carbonyl carbons whereas Marine DOM was markedly enriched in alkoxy carbon (e.g., carbohydrate-like moieties). Both samples contained significant amide N, but Coastal DOM had nitrogen bonded to aromatic carbons. Our dipolar-dephased spectra indicated that a large fraction of alkoxy carbons were not protonated. For Coastal DOM, our NMR results were consistent with the presence of the major structural units of (1) carbohydrate-like moieties, (2) lignin residues, (3) peptides or amino sugars, and (4) COO-bonded alkyls. For Marine DOM, they were (1) carbohydrate-like moieties, (2) peptides or amino sugars, and (3) COO-bonded alkyls. In addition, both samples contained significant amounts of nonpolar alkyl groups. The potential sources of the major structural units of DOM were discussed in detail. Nonprotonated O-alkyl carbon content was proposed as a possible index of humification. PMID:22553962

  16. Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

    SciTech Connect

    Soudackov, Alexander V.; Hammes-Schiffer, Sharon

    2015-11-21

    Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency proton donor-acceptor vibrational modes. These rate constants differ from previous rate constants derived with the cumulant expansion approach in that the logarithmic expansion of the vibronic coupling in terms of the proton donor-acceptor distance includes a quadratic as well as a linear term. The analysis illustrates that inclusion of this quadratic term in the framework of the cumulant expansion framework may significantly impact the rate constants at high temperatures for proton transfer interfaces with soft proton donor-acceptor modes that are associated with small force constants and weak hydrogen bonds. The effects of the quadratic term may also become significant in these regimes when using the vibronic coupling expansion in conjunction with a thermal averaging procedure for calculating the rate constant. In this case, however, the expansion of the coupling can be avoided entirely by calculating the couplings explicitly for the range of proton donor-acceptor distances sampled. The effects of the quadratic term for weak hydrogen-bonding systems are less significant for more physically realistic models that prevent the sampling of unphysical short proton donor-acceptor distances. Additionally, the rigorous relation between the cumulant expansion and thermal averaging approaches is clarified. In particular, the cumulant expansion rate constant includes effects from dynamical interference between the proton donor-acceptor and solvent motions and becomes equivalent to the thermally averaged rate constant when these dynamical effects are neglected. This analysis identifies the regimes in which each rate constant expression is valid and thus will be important for future applications to proton

  17. Insights into Proton-Coupled Electron Transfer from Computation

    NASA Astrophysics Data System (ADS)

    Provorse, Makenzie R.

    Proton-coupled electron transfer (PCET) is utilized throughout Nature to facilitate essential biological processes, such as photosynthesis, cellular respiration, and DNA replication and repair. The general approach to studying PCET processes is based on a two-dimensional More O'Ferrall-Jencks diagram in which electron transfer (ET) and proton transfer (PT) occur in a sequential or concerted fashion. Experimentally, it is difficult to discern the contributing factors of concerted PCET mechanisms. Several theoretical approaches have arisen to qualitatively and quantitatively investigate these reactions. Here, we present a multistate density functional theory (MSDFT) method to efficiently and accurately model PCET mechanisms. The MSDFT method is validated against experimental and computational data previously reported on an isoelectronic series of small molecule self-exchange hydrogen atom transfer reactions and a model complex specifically designed to study long-range ET through a hydrogen-bonded salt-bridge interface. Further application of this method to the hydrogen atom abstraction of ascorbate by a nitroxyl radical demonstrates the sensitivity of the thermodynamic and kinetic properties to solvent effects. In particular, the origin of the unusual kinetic isotope effect is investigated. Lastly, the MSDFT is employed in a combined quantum mechanical/molecular mechanical (QM/MM) approach to explicitly model PCET in condensed phases.

  18. Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

    SciTech Connect

    Soudackov, Alexander; Hammes-Schiffer, Sharon

    2015-11-17

    Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency regimes for the proton donor-acceptor vibrational mode. These rate constants differ from previous rate constants derived with the cumulant expansion approach in that the logarithmic expansion of the vibronic coupling in terms of the proton donor-acceptor distance includes a quadratic as well as a linear term. The analysis illustrates that inclusion of this quadratic term does not significantly impact the rate constants derived using the cumulant expansion approach in any of the regimes studied. The effects of the quadratic term may become significant when using the vibronic coupling expansion in conjunction with a thermal averaging procedure for calculating the rate constant, however, particularly at high temperatures and for proton transfer interfaces with extremely soft proton donor-acceptor modes that are associated with extraordinarily weak hydrogen bonds. Even with the thermal averaging procedure, the effects of the quadratic term for weak hydrogen-bonding systems are less significant for more physically realistic models that prevent the sampling of unphysical short proton donor-acceptor distances, and the expansion of the coupling can be avoided entirely by calculating the couplings explicitly for the range of proton donor-acceptor distances. This analysis identifies the regimes in which each rate constant expression is valid and thus will be important for future applications to proton transfer and proton-coupled electron transfer in chemical and biological processes. We are grateful for support from National Institutes of Health Grant GM056207 (applications to enzymes) and the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy

  19. Gating Topology of the Proton-Coupled Oligopeptide Symporters

    PubMed Central

    Fowler, Philip W.; Orwick-Rydmark, Marcella; Radestock, Sebastian; Solcan, Nicolae; Dijkman, Patricia M.; Lyons, Joseph A.; Kwok, Jane; Caffrey, Martin; Watts, Anthony; Forrest, Lucy R.; Newstead, Simon

    2015-01-01

    Summary Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport through rearrangement of their two six-helix bundles around a central ligand binding site; how this is achieved, however, is poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we present a detailed study of the transport dynamics of two bacterial oligopeptide transporters, PepTSo and PepTSt. Our results identify several salt bridges that stabilize outward-facing conformations and we show that, for all the current structures of MFS transporters, the first two helices of each of the four inverted-topology repeat units form half of either the periplasmic or cytoplasmic gate and that these function cooperatively in a scissor-like motion to control access to the peptide binding site during transport. PMID:25651061

  20. Proton-Coupled Electron Transfer: Moving Together and Charging Forward.

    PubMed

    Hammes-Schiffer, Sharon

    2015-07-22

    Proton-coupled electron transfer (PCET) is ubiquitous throughout chemistry and biology. This Perspective discusses recent advances and current challenges in the field of PCET, with an emphasis on the role of theory and computation. The fundamental theoretical concepts are summarized, and expressions for rate constants and kinetic isotope effects are provided. Computational methods for calculating reduction potentials and pKa's for molecular electrocatalysts, as well as insights into linear correlations and non-innocent ligands, are also described. In addition, computational methods for simulating the nonadiabatic dynamics of photoexcited PCET are discussed. Representative applications to PCET in solution, proteins, electrochemistry, and photoinduced processes are presented, highlighting the interplay between theoretical and experimental studies. The current challenges and suggested future directions are outlined for each type of application, concluding with an overall view to the future. PMID:26110700

  1. Proton-Coupled Electron Transfer: Moving Together and Charging Forward

    PubMed Central

    2016-01-01

    Proton-coupled electron transfer (PCET) is ubiquitous throughout chemistry and biology. This Perspective discusses recent advances and current challenges in the field of PCET, with an emphasis on the role of theory and computation. The fundamental theoretical concepts are summarized, and expressions for rate constants and kinetic isotope effects are provided. Computational methods for calculating reduction potentials and pKa’s for molecular electrocatalysts, as well as insights into linear correlations and non-innocent ligands, are also described. In addition, computational methods for simulating the nonadiabatic dynamics of photoexcited PCET are discussed. Representative applications to PCET in solution, proteins, electrochemistry, and photoinduced processes are presented, highlighting the interplay between theoretical and experimental studies. The current challenges and suggested future directions are outlined for each type of application, concluding with an overall view to the future. PMID:26110700

  2. Influence of the incorporation of fibers in biscuit dough on proton mobility characterized by time domain NMR.

    PubMed

    Serial, M R; Blanco Canalis, M S; Carpinella, M; Valentinuzzi, M C; León, A E; Ribotta, P D; Acosta, R H

    2016-02-01

    The effect of fiber addition on the distribution and mobility of protons in biscuits is studied by using low resolution time domain nuclear magnetic resonance (TD-NMR). The proportion of flour is reduced in order to incorporate inulin and oat fiber. NMR temperature dependent experiments are carried out in order to gain insight on the processes occurring in biscuit baking. Proton populations were identified measuring spin-spin relaxation times (T2). The major change in the relaxation profiles upon incorporation of fibers corresponds to mobile water molecules, which appear to be related to dough spreading behavior and biscuit quality. Biscuit samples baked in a commercial oven were studied by two dimensional spin-lattice/spin-spin (T1-T2) relaxation maps. The T1/T2 ratio is used as an indicator of the population mobility, where changes in the mobility of water in contact with flour components as starch, proteins and pentosans are observed. PMID:26304434

  3. Rapid amide proton exchange rates in peptides and proteins measured by solvent quenching and two-dimensional NMR.

    PubMed Central

    Zhang, Y. Z.; Paterson, Y.; Roder, H.

    1995-01-01

    In an effort to develop a more versatile quenched hydrogen exchange method for studies of peptide conformation and protein-ligand interactions, the mechanism of amide proton exchange for model peptides in DMSO-D2O mixtures was investigated by NMR methods. As in water, H-D exchange rates in the presence of 90% or 95% DMSO exhibit characteristic acid- and base-catalyzed processes and negligible water catalysis. However, the base-catalyzed rate is suppressed by as much as four orders of magnitude in 95% DMSO. As a result, the pH at which the exchange rate goes through a minimum is shifted up by about two pH units and the minimum exchange rate is approximately 100-fold reduced relative to that in D2O. The solvent-dependent decrease in base-catalyzed exchange rates can be attributed primarily to a large increase in pKa values for the NH group, whereas solvent effects on pKW seem less important. Addition of toluene and cyclohexane resulted in improved proton NMR chemical shift dispersion. The dramatic reduction in exchange rates observed in the solvent mixture at optimal pH makes it possible to apply 2D NMR for NH exchange measurements on peptides under conditions where rates are too rapid for direct NMR analysis. To test this solvent-quenching method, melittin was exchanged in D2O (pH 3.2, 12 degrees C), aliquots were quenched by rapid freezing, lyophilized, and dissolved in quenching buffer (70% DMSO, 25% toluene, 4% D2O, 1% cyclohexane, 75 mM dichloroacetic acid) for NMR analysis. Exchange rates for 21 amide protons were measured by recording 2D NMR spectra on a series of samples quenched at different times. The results are consistent with a monomeric unfolded conformation of melittin at acidic pH. The ability to trap labile protons by solvent quenching makes it possible to extend amide protection studies to peptide ligands or labile protons on the surface of a protein involved in macromolecular interactions. PMID:7613478

  4. Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance ((1) H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS).

    PubMed

    Paiva, C; Amaral, A; Rodriguez, M; Canyellas, N; Correig, X; Ballescà, J L; Ramalho-Santos, J; Oliva, R

    2015-05-01

    The objective of this study was to contribute to the first comprehensive metabolomic characterization of the human sperm cell through the application of two untargeted platforms based on proton nuclear magnetic resonance ((1) H-NMR) spectroscopy and gas chromatography coupled to mass spectrometry (GC-MS). Using these two complementary strategies, we were able to identify a total of 69 metabolites, of which 42 were identified using NMR, 27 using GC-MS and 4 by both techniques. The identity of some of these metabolites was further confirmed by two-dimensional (1) H-(1) H homonuclear correlation spectroscopy (COSY) and (1) H-(13) C heteronuclear single-quantum correlation (HSQC) spectroscopy. Most of the metabolites identified are reported here for the first time in mature human spermatozoa. The relationship between the metabolites identified and the previously reported sperm proteome was also explored. Interestingly, overrepresented pathways included not only the metabolism of carbohydrates, but also of lipids and lipoproteins. Of note, a large number of the metabolites identified belonged to the amino acids, peptides and analogues super class. The identification of this initial set of metabolites represents an important first step to further study their function in male gamete physiology and to explore potential reasons for dysfunction in future studies. We also demonstrate that the application of NMR and MS provides complementary results, thus constituting a promising strategy towards the completion of the human sperm cell metabolome. PMID:25854681

  5. Assignments of proton populations in dough and bread using NMR relaxometry of starch, gluten, and flour model systems.

    PubMed

    Bosmans, Geertrui M; Lagrain, Bert; Deleu, Lomme J; Fierens, Ellen; Hills, Brian P; Delcour, Jan A

    2012-05-30

    Starch-water, gluten-water, and flour-water model systems as well as straight-dough bread were investigated with (1)H NMR relaxometry using free induction decay and Carr-Purcell-Meiboom-Gill pulse sequences. Depending on the degree of interaction between polymers and water, different proton populations could be distinguished. The starch protons in the starch-water model gain mobility owing to amylopectin crystal melting, granule swelling, and amylose leaching, whereas water protons lose mobility due to increased interaction with starch polymers. Heating of the gluten-water sample induces no pronounced changes in proton distributions. Heating changes the proton distributions of the flour-water and starch-water models in a similar way, implying that the changes are primarily attributable to starch gelatinization. Proton distributions of the heated flour-water model system and those of fresh bread crumb are very similar. This allows identifying the different proton populations in bread on the basis of the results from the model systems. PMID:22553963

  6. Visualizing Unresolved Scalar Couplings by Real-Time J-Upscaled NMR

    PubMed Central

    2015-01-01

    Scalar coupling patterns contain a wealth of structural information. The determination, especially of small scalar coupling constants, is often prevented by merging the splittings with the signal line width. Here we show that real-time J-upscaling enables the visualization of unresolved coupling constants in the acquisition dimension of one-dimensional (1D) or multidimensional NMR spectra. This technique, which works by introducing additional scalar coupling evolution delays within the recording of the FID (free induction decay), not only stretches the recorded coupling patterns but also actually enhances the resolution of multiplets, by reducing signal broadening by magnetic field inhomogeneities during the interrupted data acquisition. Enlarging scalar couplings also enables their determination in situations where the spectral resolution is limited, such as in the acquisition dimension of heteronuclear broadband decoupled HSQC (heteronuclear single quantum correlation) spectra. PMID:25837306

  7. Single-Quantum Coherence Filter for Strongly Coupled Spin Systems for Localized 1H NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Trabesinger, Andreas H.; Mueller, D. Christoph; Boesiger, Peter

    2000-08-01

    A pulse sequence for localized in vivo1H NMR spectroscopy is presented, which selectively filters single-quantum coherence built up by strongly coupled spin systems. Uncoupled and weakly coupled spin systems do not contribute to the signal output. Analytical calculations using a product operator description of the strongly coupled AB spin system as well as in vitro tests demonstrate that the proposed filter produces a signal output for a strongly coupled AB spin system, whereas the resonances of a weakly coupled AX spin system and of uncoupled spins are widely suppressed. As a potential application, the detection of the strongly coupled AA‧BB‧ spin system of taurine at 1.5 T is discussed.

  8. Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR Spectroscopy.

    PubMed

    Juen, Michael Andreas; Wunderlich, Christoph Hermann; Nußbaumer, Felix; Tollinger, Martin; Kontaxis, Georg; Konrat, Robert; Hansen, D Flemming; Kreutz, Christoph

    2016-09-19

    In this work an improved stable isotope labeling protocol for nucleic acids is introduced. The novel building blocks eliminate/minimize homonuclear (13) C and (1) H scalar couplings thus allowing proton relaxation dispersion (RD) experiments to report accurately on the chemical exchange of nucleic acids. Using site-specific (2) H and (13) C labeling, spin topologies are introduced into DNA and RNA that make (1) H relaxation dispersion experiments applicable in a straightforward manner. The novel RNA/DNA building blocks were successfully incorporated into two nucleic acids. The A-site RNA was previously shown to undergo a two site exchange process in the micro- to millisecond time regime. Using proton relaxation dispersion experiments the exchange parameters determined earlier could be recapitulated, thus validating the proposed approach. We further investigated the dynamics of the cTAR DNA, a DNA transcript that is involved in the viral replication cycle of HIV-1. Again, an exchange process could be characterized and quantified. This shows the general applicablility of the novel labeling scheme for (1) H RD experiments of nucleic acids. PMID:27533469

  9. Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins

    NASA Astrophysics Data System (ADS)

    Chevelkov, Veniamin; Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam

    2014-05-01

    Proton-detected solid-state NMR was applied to a highly deuterated insoluble, non-crystalline biological assembly, the Salmonella typhimurium type iii secretion system (T3SS) needle. Spectra of very high resolution and sensitivity were obtained at a low protonation level of 10-20% at exchangeable amide positions. We developed efficient experimental protocols for resonance assignment tailored for this system and the employed experimental conditions. Using exclusively dipolar-based interspin magnetization transfers, we recorded two sets of 3D spectra allowing for an almost complete backbone resonance assignment of the needle subunit PrgI. The additional information provided by the well-resolved proton dimension revealed the presence of two sets of resonances in the N-terminal helix of PrgI, while in previous studies employing 13C detection only a single set of resonances was observed.

  10. Scalar Relativistic Computations and Localized Orbital Analyses of Nuclear Hyperfine Coupling and Paramagnetic NMR Chemical Shifts

    SciTech Connect

    Aquino, Fredy W.; Pritchard, Ben; Autschbach, Jochen

    2012-02-14

    A method is reported by which calculated hyperfine coupling constants (HFCCs) and paramagnetic NMR (pNMR) chemical shifts can be analyzed in a chemically intuitive way by decomposition into contributions from localized molecular orbitals (LMOs). A new module for density functional calculations with nonhybrid functionals, global hybrids, and range-separated hybrids, utilizing the two-component relativistic zeroth-order regular approximation (ZORA), has been implemented in the parallel open-source NWChem quantum chemistry package. Benchmark results are reported for a test set of few-atom molecules with light and heavy elements. Finite nucleus effects on ¹⁹⁹Hg HFCCs are shown to be on the order of -11 to -15%. A proof of concept for the LMO analysis is provided for the metal and fluorine HFCCs of TiF₃ and NpF₆. Calculated pNMR chemical shifts are reported for the 2-methylphenyl-t-butylnitroxide radical and for five cyclopentadienyl (Cp) sandwich complexes with 3d metals. Nickelocene and vanadocene carbon pNMR shifts are analyzed in detail, demonstrating that the large carbon pNMR shifts calculated as +1540 for Ni (exptl.: +1514) and -443 for V (exptl.: -510) are caused by different spin-polarization mechanisms. For Ni, Cp to Ni π back-donation dominates the result, whereas for vanadocene, V to Cp σ donation with relaxation of the carbon 1s shells can be identified as the dominant mechanism.

  11. Two-pulse NMR techniques for studying proton-unpaired electron interactions in coals and chars

    NASA Astrophysics Data System (ADS)

    Barton, W. A.; Lynch, L. J.

    The time-domain NMR signals stimulated in solids by two-pulse sequences of the form 90°- τ- βφ, where β is the angle of rotation and φ the relative phase of the second pulse which is separated from the initial 90° pulse by a time τ, can be influenced by the presence of a second spin species and therefore, in principle, can yield information on the separate contributions, M2II and M2IS, of like- and unlike-spin interactions to the Van Vleck second moment M2I of the resonant spins. The validity of the standard operator formalism for predicting the transverse magnetization signals thus produced in homogeneous solids by the 90°- τ-90 φ° and 90°- τ-180 φ° ( φ = 0° and 90°) sequences is discussed and the effects of pulse duration are briefly outlined. The time-series expansions yielded by the operator formalism for these signals are reviewed with emphasis on the effects of unlike-spin interactions, and a useful difference signal is discussed. The potential for application of these two-pulse techniques to protons in heterogeneous solids such as coals, in which unpaired electrons constitute the second spin species, is considered and experimentally assessed. Semiquantitative estimates of M2IS are made for protons in diphenyl picryl hydrazyl (DPPH) and several coals and chars at room temperature from measurements of the amplitude of the 90°- τ-90° 0 ° transient signal at small τ and of the initial rate of attenuation of the 90°- τ-90 90°° solid echo with increasing τ. It is found that (i) organic radicals and paramagnetic ions produce relatively small M2IS values, a result which limits the usefulness of this approach to studying unpaired electron properties of coals and chars; (ii) the M2II values deduced from these results and calculations of M2I follow expected trends; and (iii) only specimens containing small particles of magnetically ordered material give rise to rapidly decaying time-domain signals and a well-defined 90°- τ-180 90°° spin

  12. Complete thermodynamic characterization of the multiple protonation equilibria of the aminoglycoside antibiotic paromomycin: a calorimetric and natural abundance 15N NMR study.

    PubMed

    Barbieri, Christopher M; Pilch, Daniel S

    2006-02-15

    The binding of aminoglycoside antibiotics to a broad range of macromolecular targets is coupled to protonation of one or more of the amino groups that typify this class of drugs. Determining how and to what extent this linkage influences the energetics of the aminoglycoside-macromolecule binding reaction requires a detailed understanding of the thermodynamics associated with the protonation equilibria of the aminoglycoside amino groups. In recognition of this need, a calorimetric- and NMR-based approach for obtaining the requisite thermodynamic information is presented using paromomycin as the model aminoglycoside. Temperature- and pH-dependent 15N NMR studies provide pK(a) values for the five paromomycin amino groups, as well as the temperature dependence of these pK(a) values. These studies also indicate that the observed pK(a) values associated with the free base form of paromomycin are lower in magnitude than the corresponding values associated with the sulfate salt form of the drug. This difference in pK(a) is due to drug interactions with the sulfate counterions at the high drug concentrations (> or = 812 mM) used in the 15N NMR studies. Isothermal titration calorimetry studies conducted at drug concentrations < or = 45 microM reveal that the extent of paromomycin protonation linked to the binding of the drug to its pharmacologically relevant target, the 16 S rRNA A-site, is consistent with the pK(a) values of the free base and not the sulfate salt form of the drug. Temperature- and pH-dependent isothermal titration calorimetry studies yield exothermic enthalpy changes (deltaH) for protonation of the five paromomycin amino groups, as well as positive heat capacity changes (deltaC(p)) for three of the five amino groups. Regarded as a whole, the results presented here represent an important first step toward establishing a thermodynamic database that can be used to predict how aminoglycoside-macromolecule binding energetics will be influenced by conditions such

  13. A General Method for Extracting Individual Coupling Constants from Crowded (1)H NMR Spectra.

    PubMed

    Sinnaeve, Davy; Foroozandeh, Mohammadali; Nilsson, Mathias; Morris, Gareth A

    2016-01-18

    Couplings between protons, whether scalar or dipolar, provide a wealth of structural information. Unfortunately, the high number of (1)H-(1)H couplings gives rise to complex multiplets and severe overlap in crowded spectra, greatly complicating their measurement. Many different methods exist for disentangling couplings, but none approaches optimum resolution. Here, we present a general new 2D J-resolved method, PSYCHEDELIC, in which all homonuclear couplings are suppressed in F2, and only the couplings to chosen spins appear, as simple doublets, in F1. This approaches the theoretical limit for resolving (1)H-(1)H couplings, with close to natural linewidths and with only chemical shifts in F2. With the same high sensitivity and spectral purity as the parent PSYCHE pure shift experiment, PSYCHEDELIC offers a robust method for chemists seeking to exploit couplings for structural, conformational, or stereochemical analyses. PMID:26636773

  14. Solid-State NMR Investigation of the Conformation, Proton Conduction, and Hydration of the Influenza B Virus M2 Transmembrane Proton Channel.

    PubMed

    Williams, Jonathan K; Tietze, Daniel; Lee, Myungwoon; Wang, Jun; Hong, Mei

    2016-07-01

    Together with the influenza A virus, influenza B virus causes seasonal flu epidemics. The M2 protein of influenza B (BM2) forms a tetrameric proton-conducting channel that is important for the virus lifecycle. BM2 shares little sequence homology with AM2, except for a conserved HxxxW motif in the transmembrane (TM) domain. Unlike AM2, no antiviral drugs have been developed to block the BM2 channel. To elucidate the proton-conduction mechanism of BM2 and to facilitate the development of BM2 inhibitors, we have employed solid-state NMR spectroscopy to investigate the conformation, dynamics, and hydration of the BM2 TM domain in lipid bilayers. BM2 adopts an α-helical conformation in lipid membranes. At physiological temperature and low pH, the proton-selective residue, His19, shows relatively narrow (15)N chemical exchange peaks for the imidazole nitrogens, indicating fast proton shuttling that interconverts cationic and neutral histidines. Importantly, pH-dependent (15)N chemical shifts indicate that His19 retains the neutral population to much lower pH than His37 in AM2, indicating larger acid-dissociation constants or lower pKa's. We attribute these dynamical and equilibrium differences to the presence of a second titratable histidine, His27, which may increase the proton-dissociation rate of His19. Two-dimensional (1)H-(13)C correlation spectra probing water (1)H polarization transfer to the peptide indicates that the BM2 channel becomes much more hydrated at low pH than at high pH, particularly at Ser12, indicating that the pore-facing serine residues in BM2 mediate proton relay to the proton-selective histidine. PMID:27286559

  15. Using magnetic coupling to implement 1H, 19F, 13C experiments in routine high resolution NMR probes

    NASA Astrophysics Data System (ADS)

    Bowyer, Paul; Finnigan, Jim; Marsden, Brian; Taber, Bob; Zens, Albert

    2015-12-01

    We report in this paper the design of 1H, 19F, 13C circuitry using magnetic coupling which can do on demand experiments where one of the three nuclei is observed and the other two are decoupled. The implementation of this circuitry in routine NMR probes is compared with capacitive coupling methods where it was found that by using magnetic coupling the performance of the routine NMR probe was not impacted by the addition of this circuitry. It is surmised that using this type of circuitry would be highly desirable for those chemists doing routine 19F NMR.

  16. Synthetic Applications of Proton-Coupled Electron Transfer.

    PubMed

    Gentry, Emily C; Knowles, Robert R

    2016-08-16

    Redox events in which an electron and proton are exchanged in a concerted elementary step are commonly referred to as proton-coupled electron transfers (PCETs). PCETs are known to operate in numerous important biological redox processes, as well as recent inorganic technologies for small molecule activation. These studies suggest that PCET catalysis might also function as a general mode of substrate activation in organic synthesis. Over the past three years, our group has worked to advance this hypothesis and to demonstrate the synthetic utility of PCET through the development of novel catalytic radical chemistries. The central aim of these efforts has been to demonstrate the ability of PCET to homolytically activate a wide variety of common organic functional groups that are energetically inaccessible using known molecular H atom transfer catalysts. To do so, we made use of a simple formalism first introduced by Mayer and co-workers that allowed us to predict the thermodynamic capacity of any oxidant/base or reductant/acid pair to formally add or remove H· from a given substrate. With this insight, we were able to rationally select catalyst combinations thermodynamically competent to homolyze the extraordinarily strong E-H σ-bonds found in many common protic functional groups (BDFEs > 100 kcal/mol) or to form unusually weak bonds to hydrogen via the reductive action of common organic π-systems (BDFEs < 35 kcal/mol). These ideas were reduced to practice through the development of new catalyst systems for reductive PCET activations of ketones and oxidative PCET activation of amide N-H bonds to directly furnish reactive ketyl and amidyl radicals, respectively. In both systems, the reaction outcomes were found to be successfully predicted using the effective bond strength formalism, suggesting that these simple thermochemical considerations can provide useful and actionable insights into PCET reaction design. The ability of PCET catalysis to control

  17. Proton-Coupled Electron Transfer: Moving Together and Charging Forward

    SciTech Connect

    Hammes-Schiffer, Sharon

    2015-06-25

    Proton-coupled electron transfer (PCET) is ubiquitous throughout chemistry and biology. This Perspective discusses recent advances and current challenges in the field of PCET, with an emphasis on the role of theory and computation. The fundamental theoretical concepts are summarized, and expressions for rate constants and kinetic isotope effects are provided. Computational methods for calculating reduction potentials and pKa’s for molecular electrocatalysts, as well as methods for simulating the nonadiabatic dynamics of photoinduced processes, are also described. Representative applications to PCET in solution, proteins, electrochemistry, and photoinduced processes are presented, highlighting the interplay between theoretical and experimental studies. The current challenges and suggested future directions are outlined for each type of application, concluding with an overall view to the future. The work described herein was supported by National Science Foundation Grant CHE-13-61293 (theory development), National Institutes of Health Grant GM056207 (soybean lipoxygenase), Center for Chemical Innovation of the National Science Foundation Solar Fuels Grant CHE-1305124 (cobalt catalysts), Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences (nickel catalysts), and Air Force Office of Scientific Research Award No. FA9550-14-1-0295 (photoinduced PCET).

  18. Improving the Mass-Limited Performance of Routine NMR Probes using Coupled Coils.

    PubMed

    Marsden, Brian; Lim, Victor; Taber, Bob; Zens, Albert

    2016-07-01

    We report a method to convert, on demand, a general use dual-broadband probe to a high performance mass-limited probe for both high band and low band nuclei. This technology uses magnetic coupling of inductors to achieve this capability. The method offers a cost effective way of increasing the performance of routine NMR probes without having to change probes or increase the overall foot print of the spectrometer. PMID:27155588

  19. Improving the Mass-Limited Performance of Routine NMR Probes using Coupled Coils

    NASA Astrophysics Data System (ADS)

    Marsden, Brian; Lim, Victor; Taber, Bob; Zens, Albert

    2016-07-01

    We report a method to convert, on demand, a general use dual-broadband probe to a high performance mass-limited probe for both high band and low band nuclei. This technology uses magnetic coupling of inductors to achieve this capability. The method offers a cost effective way of increasing the performance of routine NMR probes without having to change probes or increase the overall foot print of the spectrometer.

  20. The HN(COCA)HAHB NMR experiment for the stereospecific assignment of Hbeta-protons in non-native states of proteins.

    PubMed

    Hähnke, Martin J; Richter, Christian; Heinicke, Friederike; Schwalbe, Harald

    2010-01-27

    (3)J(H(alpha),H(beta))-coupling constants deliver precious information on the population of the three favored chi(1)-rotamers in unfolded states of proteins. Here, a novel pulse sequence, tailored toward the NMR analysis of non-native states of proteins, the HN(COCA)HAHB experiment, is developed to measure (3)J(H(alpha),H(beta)). In four subsequent INEPT steps, magnetization is transferred from H(N) to H(alpha). In a COSY-like magnetization transfer step, dephasing of magnetization on H(alpha) is quantified to determine the (3)J(H(alpha),H(beta))-coupling constants. Analysis of the measured homonuclear coupling constants, together with measurement of heteronuclear (3)J(N,C(gamma))- and (3)J(C',C(gamma))-coupling constants, allows stereospecific assignment of the two diastereotopic H(beta)-protons even in unfolded states of proteins, and the derivation of populations according to a Pachler-type analysis. PMID:20039672

  1. Measurement of nuclear magnetic dipole—dipole couplings in magic angle spinning NMR

    NASA Astrophysics Data System (ADS)

    Tycko, Robert; Dabbagh, Gary

    1990-10-01

    We describe a method for measuring nuclear magnetic dipole—dipole couplings in NMR spectra of solids undergoing rapid magic angle spinning (MAS). We show in theory, simulations, and experiments that the couplings, which are averaged out by MAS alone, can be recovered by applying simple resonant radiofrequency pulse sequences in synchrony with the sample rotation. Experimental 13C dipolar powder pattern spectra of polycrystalline ( 13CH 3) 2C(OH)SO 3Na obtained in a two-dimensional experiment based on this method are presented. The method provides a means of determining internuclear distances in polycrystalline and noncrystalline solids while retaining the high resolution and sensitivity afforded by MAS.

  2. Novel macrocyclic carriers for proton-coupled liquid membrane transport. Final report

    SciTech Connect

    Lamb, J.D.; Izatt, R.M.; Bradshaw, J.S.; Shirts, R.B.

    1996-08-24

    The objective of this research program is to elucidate the chemical principles which are responsible for the cation selectivity and permeability of liquid membranes containing macrocyclic carriers. Several new macrocyclic carriers were synthesized during the last three year period. In addition, new, more convenient synthetic routes were achieved for several nitrogen-containing bicyclic and tricyclic macrocycles. The cation binding properties of these macrocycles were investigated by potentiometric titration, calorimetric titration, solvent extraction and NMR techniques. In addition, hydrophobic macrocycles were incorporated into dual hollow fiber and other membrane systems to investigate their membrane performance, especially in the proton-coupled transport mode. A study of the effect of methoxyalkyl macrocycle substituents on metal ion transport was completed. A new calorimeter was constructed which made it possible to study the thermodynamics of macrocycle-cation binding to very high temperatures. Measurements of thermodynamic data for the interaction of crown ethers with alkali and alkaline earth cations were achieved to 473 K. Molecular modeling work was begun for the first time on this project and fundamental principles were identified and developed for the establishment of working models in the future.

  3. Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping.

    PubMed

    Dona, Anthony C; Jiménez, Beatriz; Schäfer, Hartmut; Humpfer, Eberhard; Spraul, Manfred; Lewis, Matthew R; Pearce, Jake T M; Holmes, Elaine; Lindon, John C; Nicholson, Jeremy K

    2014-10-01

    Proton nuclear magnetic resonance (NMR)-based metabolic phenotyping of urine and blood plasma/serum samples provides important prognostic and diagnostic information and permits monitoring of disease progression in an objective manner. Much effort has been made in recent years to develop NMR instrumentation and technology to allow the acquisition of data in an effective, reproducible, and high-throughput approach that allows the study of general population samples from epidemiological collections for biomarkers of disease risk. The challenge remains to develop highly reproducible methods and standardized protocols that minimize technical or experimental bias, allowing realistic interlaboratory comparisons of subtle biomarker information. Here we present a detailed set of updated protocols that carefully consider major experimental conditions, including sample preparation, spectrometer parameters, NMR pulse sequences, throughput, reproducibility, quality control, and resolution. These results provide an experimental platform that facilitates NMR spectroscopy usage across different large cohorts of biofluid samples, enabling integration of global metabolic profiling that is a prerequisite for personalized healthcare. PMID:25180432

  4. Thermal coupling of protons and neutral hydrogen with anisotropic temperatures in the fast solar wind

    NASA Astrophysics Data System (ADS)

    Allen, Lorraine A.; Habbal, Shadia R.; Li, Xing

    2000-10-01

    The thermal coupling between the neutral hydrogen and protons in the inner corona is explored by extending the study of Allenet al. [1998] to include anisotropic proton temperature to determine what the neutral hydrogen Ly α spectral line measurements reveal about the proton temperature, temperature anisotropy, and outflow velocity in the fast solar wind. The anisotropic proton temperature is produced by ion cyclotron resonant interaction of protons with high-frequency waves, produced by a nonlinear cascade at the Kolmogorov dissipation rate from dominant lower-frequency Alfvén waves. As a result of the coupling between the respective parallel and perpendicular components of the neutral hydrogen and proton temperatures, a greater temperature anisotropy in the neutral hydrogen develops as compared to the case when the proton temperature is isotropic. The neutral hydrogen and proton effective temperatures (Teff), incorporating both random and wave motions of the particles, and outflow velocities, are comparable below ~3Rs. Neutral hydrogen anisotropy ratios, TH(eff)/T∥, ~4 below 3Rs are readily attained, in agreement with observations. Below ~3Rs, these reflect the proton anisotropy ratio. For plasma conditions typical of the fast solar wind, these results imply that the measured Ly α spectral line profiles, from which the neutral hydrogen temperature, anisotropy ratio, and outflow velocity are inferred, are equivalent to measurements of protons below ~3Rs. Beyond this distance the width of the measured Ly α spectral lines provides a lower limit to the proton effective temperature and temperature anisotropy in the inner corona.

  5. Multicomponent analysis of radiolytic products in human body fluids using high field proton nuclear magnetic resonance (NMR) spectroscopy

    NASA Astrophysics Data System (ADS)

    Grootveld, Martin C.; Herz, Herman; Haywood, Rachel; Hawkes, Geoffrey E.; Naughton, Declan; Perera, Anusha; Knappitt, Jacky; Blake, David R.; Claxson, Andrew W. D.

    1994-05-01

    High field proton Hahn spin-echo nuclear magnetic resonance (NMR) spectroscopy has been employed to investigate radiolytic damage to biomolecules present in intact human body fluids. γ-Radiolysis of healthy or rheumatoid human serum (5.00 kGy) in the presence of atmospheric O 2 gave rise to reproducible elevations in the concentration of NMR-detectable acetate which are predominantly ascribable to the prior oxidation of lactate to pyruvate by hydroxyl radical (·OH) followed by oxidative decarboxylation of pyruvate by radiolytically-generated hydrogen peroxide (H 2O 2) and/or further ·OH radical. Increases in the serum levels of non-protein-bound, low-molecular-mass components such as citrate and glutamine were also observed subsequent to γ-radiolysis, an observation which may reflect their mobilisation from protein binding-sites by ·OH radical, superoxide anion and/or H 2O 2. Moreover, substantial radiolytically-mediated elevations in the concentration of serum formate were also detectable. In addition to the above modifications, γ-radiolysis of inflammatory knee-joint synovial fluid (SF) generated a low-molecular-mass oligosaccharide species derived from the radiolytic fragmentation of hyaluronate. The radiolytically-mediated production of acetate in SF samples was markedly greater than that observed in serum samples, a consequence of the much higher levels of ·OH radical-scavenging lactate present. Indeed, increases in SF acetate concentration were detectable at doses as low as 48 Gy. We conclude that high field proton NMR analysis provides much useful information regarding the relative radioprotectant abilities of endogenous components and the nature, status and levels of radiolytic products generated in intact biofluids. We also suggest that NMR-detectable radiolytic products with associated toxicological properties (e.g. formate) may play a role in contributing to the deleterious effects observed following exposure of living organisms to sources of

  6. Proton NMR studies on the covalently linked RNA-DNA hybrid r(GCG)d(TATACGC). Assignment of proton resonances by application of the nuclear Overhauser effect.

    PubMed Central

    Mellema, J R; Haasnoot, C A; van der Marel, G A; Wille, G; van Boeckel, C A; van Boom, J H; Altona, C

    1983-01-01

    Proton NMR spectra of a covalently linked self-complementary RNA X DNA hybrid, r(GCG)-d(TATACGC), are recorded in H2O and D2O. Imino proton resonances as well as the non-exchangeable base and H-1' resonances are unambiguously assigned by means of nuclear. Overhauser effect measurements. Additional information was obtained by 31P NMR and circular dichroism spectra. The RNA parts in the duplex attain full conformational purity and adopt the usual A-RNA conformation. The DNA residues opposite the RNA tract do not adopt an A-type structure completely. Their respective sugar rings still appear to possess a certain conformational freedom. The same holds true for the central d(-TATA-) sequence which forms a DNA X DNA duplex. There appears to be a structural break in this part: the first two residues, T(4) and A(5), are clearly influenced by the adjacent RNA structure, whereas residues T(6) and A(7) behave quite similar to what usually is found in DNA duplexes in aqueous solution. PMID:6193486

  7. Rapid proton-detected NMR assignment for proteins with fast magic angle spinning.

    PubMed

    Barbet-Massin, Emeline; Pell, Andrew J; Retel, Joren S; Andreas, Loren B; Jaudzems, Kristaps; Franks, W Trent; Nieuwkoop, Andrew J; Hiller, Matthias; Higman, Victoria; Guerry, Paul; Bertarello, Andrea; Knight, Michael J; Felletti, Michele; Le Marchand, Tanguy; Kotelovica, Svetlana; Akopjana, Inara; Tars, Kaspars; Stoppini, Monica; Bellotti, Vittorio; Bolognesi, Martino; Ricagno, Stefano; Chou, James J; Griffin, Robert G; Oschkinat, Hartmut; Lesage, Anne; Emsley, Lyndon; Herrmann, Torsten; Pintacuda, Guido

    2014-09-01

    Using a set of six (1)H-detected triple-resonance NMR experiments, we establish a method for sequence-specific backbone resonance assignment of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of 5-30 kDa proteins. The approach relies on perdeuteration, amide (2)H/(1)H exchange, high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling the use of automated analysis. The method is validated with five examples of proteins in different condensed states, including two microcrystalline proteins, a sedimented virus capsid, and two membrane-embedded systems. In comparison to contemporary (13)C/(15)N-based methods, this approach facilitates and accelerates the MAS NMR assignment process, shortening the spectral acquisition times and enabling the use of unsupervised state-of-the-art computational data analysis protocols originally developed for solution NMR. PMID:25102442

  8. New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella thermoaceticum metabolic profiles

    SciTech Connect

    Xue, Junfeng; Isern, Nancy G.; Ewing, R James; Liyu, Andrey V.; Sears, Jesse A.; Knapp, Harlan; Iversen, Jens; Sisk, Daniel R.; Ahring, Birgitte K.; Majors, Paul D.

    2014-06-20

    An in-situ nuclear magnetic resonance (NMR) bioreactor was developed and employed to monitor microbial metabolism under batch-growth conditions in real time. We selected Moorella thermoacetica ATCC 49707 as a test case. M. thermoacetica (formerly Clostridium thermoaceticum) is a strictly anaerobic, thermophilic, acetogenic, gram-positive bacterium with potential for industrial production of chemicals. The metabolic profiles of M. thermoacetica were characterized during growth in batch mode on xylose (a component of lignocellulosic biomass) using the new generation NMR bioreactor in combination with high-resolution, high sensitivity NMR (HR-NMR) spectroscopy. In-situ NMR measurements were performed using water-suppressed H-1 NMR spectroscopy at an NMR frequency of 500 MHz, and aliquots of the bioreactor contents were taken for 600 MHz HR-NMR spectroscopy at specific intervals to confirm metabolite identifications and expand metabolite coverage. M. thermoacetica demonstrated the metabolic potential to produce formate, ethanol and methanol from xylose, in addition to its known capability of producing acetic acid. Real-time monitoring of bioreactor conditions showed a temporary pH decrease, with a concomitant increase in formic acid during exponential growth. Fermentation experiments performed outside of the magnet showed that the strong magnetic field employed for NMR detection did not significantly affect cell metabolism. Use of the in-situ NMR bioreactor facilitated monitoring of the fermentation process in real time, enabling identification of intermediate and end-point metabolites and their correlation with pH and biomass produced during culture growth. Real-time monitoring of culture metabolism using the NMR bioreactor in combination with the HR-NMR spectroscopy will allow optimization of the metabolism of microorganisms producing valuable bioproducts.

  9. First acceleration of a proton beam in a side coupled drift tube linac

    NASA Astrophysics Data System (ADS)

    Ronsivalle, C.; Picardi, L.; Ampollini, A.; Bazzano, G.; Marracino, F.; Nenzi, P.; Snels, C.; Surrenti, V.; Vadrucci, M.; Ambrosini, F.

    2015-07-01

    We report the first experiment aimed at the demonstration of low-energy protons acceleration by a high-efficiency S-band RF linear accelerator. The proton beam has been accelerated from 7 to 11.6 MeV by a 1 meter long SCDTL (Side Coupled Drift Tube Linac) module powered with 1.3 MW. The experiment has been done in the framework of the Italian TOP-IMPLART (Oncological Therapy with Protons-Intensity Modulated Proton Therapy Linear Accelerator for Radio-Therapy) project devoted to the realization of a proton therapy centre based on a proton linear accelerator for intensity modulated cancer treatments to be installed at IRE-IFO, the largest oncological hospital in Rome. It is the first proton therapy facility employing a full linear accelerator scheme based on high-frequency technology.

  10. 1H NMR study of proton motion in hydrogen-bonded chain in Mannich base of 5,5'-dibromo-3-diethylaminomethyl-2,2'-biphenol

    NASA Astrophysics Data System (ADS)

    Wojciechowski, G.; Rozwadowski, Z.; Dziembowska, T.; Brzezinski, B.

    2001-01-01

    5,5'-dibromo-3-diethylaminomethyl-2,2'-biphenol was synthesized and the collective proton motion in two intramolecular hydrogen bonds was studied by 1H and 13C NMR as well as by FTIR spectroscopy in chloroform, acetonitrile and chloroform containing traces of water solutions. In dry chloroform, always, two separated proton signals for the two OH groups were observed. If traces of water were present at room temperature in the chloroform solution only one signal for the two OH protons was found. With decreasing temperature the collective proton motion, indicated by continuous absorption in the FTIR spectrum, was interrupted and two separate signals appeared in the 1H NMR spectrum. In acetonitrile the collective proton motion in the two intramolecular hydrogen-bonded system observed at room temperature vanished with decreasing temperature and finally only a cooperative hydrogen-bonded system, like in the solid state, was observed.

  11. Experimental study of resolution of proton chemical shifts in solids: Combined multiple pulse NMR and magic-angle spinning

    SciTech Connect

    Ryan, L.M.; Taylor, R.E.; Paff, A.J.; Gerstein, B.C.

    1980-01-01

    High-resolution nuclear magnetic resonance spectra of protons in rigid, randomly oriented solids have been measured using combined homonuclear dipolar decoupling (via multiple pulse techniques) and attenuation of chemical shift anisotropies (via magic-angle sample spinning). Under those conditions, isotropic proton chemical shifts were recorded for a variety of chemical species, with individual linewidths varying from about 55 to 110 Hz (1--2 ppm). Residual line broadening was due predominately to (i) magnetic-field instability and inhomogeneity, (ii) unresolved proton--proton spin couplings, (iii) chemical shift dispersion, (iv) residual dipolar broadening, and (v) lifetime broadening under the multiple pulse sequences used. The magnitudes of those effects and the current limits of resolution for this experiment in our spectrometer have been investigated. The compounds studied included organic solids (4, 4'-dimethylbenzophenone, 2, 6-dimethylbenzoic acid, and aspirin), polymers (polystyrene and polymethylmethacrylate), and the vitrain portion of a bituminous coal.

  12. Proton Fingerprints Portray Molecular Structures: Enhanced Description of the 1H NMR Spectra of Small Molecules

    PubMed Central

    Napolitano, José G.; Lankin, David C.; McAlpine, James B.; Niemitz, Matthias; Korhonen, Samuli-Petrus; Chen, Shao-Nong; Pauli, Guido F.

    2013-01-01

    The characteristic signals observed in NMR spectra encode essential information on the structure of small molecules. However, extracting all of this information from complex signal patterns is not trivial. This report demonstrates how computer-aided spectral analysis enables the complete interpretation of 1D 1H NMR data. The effectiveness of this approach is illustrated with a set of organic molecules, for which replicas of their 1H NMR spectra were generated. The potential impact of this methodology on organic chemistry research is discussed. PMID:24007197

  13. New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella thermoacetica metabolic profiles.

    PubMed

    Xue, Junfeng; Isern, Nancy G; Ewing, R James; Liyu, Andrei V; Sears, Jesse A; Knapp, Harlan; Iversen, Jens; Sisk, Daniel R; Ahring, Birgitte K; Majors, Paul D

    2014-10-01

    An in situ nuclear magnetic resonance (NMR) bioreactor was developed and employed to monitor microbial metabolism under batch growth conditions in real time. We selected Moorella thermoacetica ATCC 49707 as a test case. M. thermoacetica (formerly Clostridium thermoaceticum) is a strictly anaerobic, thermophilic, acetogenic, gram-positive bacterium with potential for industrial production of chemicals. The metabolic profiles of M. thermoacetica were characterized during growth in batch mode on xylose (a component of lignocellulosic biomass) using the new generation NMR bioreactor in combination with high-resolution NMR (HR-NMR) spectroscopy. In situ NMR measurements were performed using water-suppressed H-1 NMR spectroscopy at 500 MHz, and aliquots of the bioreactor contents were taken for 600-MHz HR-NMR spectroscopy at specific intervals to confirm metabolite identifications and expand metabolite coverage. M. thermoacetica demonstrated the metabolic potential to produce formate, ethanol, and methanol from xylose, in addition to its known capability of producing acetic acid. Real-time monitoring of bioreactor conditions showed a temporary pH decrease, with a concomitant increase in formic acid during exponential growth. Fermentation experiments performed outside of the magnet showed that the strong magnetic field employed for NMR detection did not significantly affect cell metabolism. Use of the in situ NMR bioreactor facilitated monitoring of the fermentation process, enabling identification of intermediate and endpoint metabolites and their correlation with pH and biomass produced during culture growth. Real-time monitoring of culture metabolism using the NMR bioreactor in combination with HR-NMR spectroscopy will allow optimization of the metabolism of microorganisms producing valuable bioproducts. PMID:24946863

  14. Communication: Proton NMR dipolar-correlation effect as a method for investigating segmental diffusion in polymer melts.

    PubMed

    Lozovoi, A; Mattea, C; Herrmann, A; Rössler, E A; Stapf, S; Fatkullin, N

    2016-06-28

    A simple and fast method for the investigation of segmental diffusion in high molar mass polymer melts is presented. The method is based on a special function, called proton dipolar-correlation build-up function, which is constructed from Hahn Echo signals measured at times t and t/2. The initial rise of this function contains additive contributions from both inter- and intramolecular magnetic dipole-dipole interactions. The intermolecular contribution depends on the relative mean squared displacements (MSDs) of polymer segments from different macromolecules, while the intramolecular part reflects segmental reorientations. Separation of both contributions via isotope dilution provides access to segmental displacements in polymer melts at millisecond range, which is hardly accessible by other methods. The feasibility of the method is illustrated by investigating protonated and deuterated polybutadiene melts with molecular mass 196 000 g/mol at different temperatures. The observed exponent of the power law of the segmental MSD is close to 0.32 ± 0.03 at times when the root MSD is in between 45 Å and 75 Å, and the intermolecular proton dipole-dipole contribution to the total proton Hahn Echo NMR signal is larger than 50% and increases with time. PMID:27369489

  15. Communication: Proton NMR dipolar-correlation effect as a method for investigating segmental diffusion in polymer melts

    NASA Astrophysics Data System (ADS)

    Lozovoi, A.; Mattea, C.; Herrmann, A.; Rössler, E. A.; Stapf, S.; Fatkullin, N.

    2016-06-01

    A simple and fast method for the investigation of segmental diffusion in high molar mass polymer melts is presented. The method is based on a special function, called proton dipolar-correlation build-up function, which is constructed from Hahn Echo signals measured at times t and t/2. The initial rise of this function contains additive contributions from both inter- and intramolecular magnetic dipole-dipole interactions. The intermolecular contribution depends on the relative mean squared displacements (MSDs) of polymer segments from different macromolecules, while the intramolecular part reflects segmental reorientations. Separation of both contributions via isotope dilution provides access to segmental displacements in polymer melts at millisecond range, which is hardly accessible by other methods. The feasibility of the method is illustrated by investigating protonated and deuterated polybutadiene melts with molecular mass 196 000 g/mol at different temperatures. The observed exponent of the power law of the segmental MSD is close to 0.32 ± 0.03 at times when the root MSD is in between 45 Å and 75 Å, and the intermolecular proton dipole-dipole contribution to the total proton Hahn Echo NMR signal is larger than 50% and increases with time.

  16. Coupling effect on the proton optics from the electron lenses

    SciTech Connect

    Luo, Y.; Gu, X.; Fischer, W.

    2010-08-01

    In this note we calculate the effect of the electron lense solenoids on the proton optics. Electron lenses (e-lenses) are to be used for head-on beam-beam compensation in the Relativistic Heavy Ion Collider (RHIC). Electron lenses are to be used for head-on beam-beam compensation in the polarized proton (pp) runs to compensate the large tune spread generated by the head-on proton-proton beam-beam interactions at IP6 and IP8 in the Relativistic Heavy Ion Collider (RHIC). The main part of an electron lens is a superconducting solenoid with a longitudinal magnetic field up to 6 T. In this report, we will estimate the e-elenses effects on the {beta} and dispersion functions with 100 GeV and 250 GeV pp run lattices. Table 1 lists some lattice and beam parameters to be used in the following study.

  17. The Synthesis and Proton NMR Spectrum of Methyl 7-Cycloheptatrienylacetate: An Advanced Undergraduate Laboratory Experiment.

    ERIC Educational Resources Information Center

    Jurch, G. R., Jr.; And Others

    1980-01-01

    Describes an advanced undergraduate laboratory experiment designed to give the senior chemistry student an opportunity to apply several synthetic and purification techniques as well as possibilities for the application of NMR spectroscopy. (CS)

  18. Guanidinoacetate methyltransferase (GAMT) deficiency diagnosed by proton NMR spectroscopy of body fluids.

    PubMed

    Engelke, Udo F H; Tassini, Maria; Hayek, Joseph; de Vries, Maaike; Bilos, Appie; Vivi, Antonio; Valensin, Gianni; Buoni, Sabrina; Zannolli, Raffaella; Brussel, Wim; Kremer, Berry; Salomons, Gajja S; Veendrick-Meekes, Monique J B M; Kluijtmans, Leo A J; Morava, Eva; Wevers, Ron A

    2009-06-01

    In patients with guanidinoacetate methyltransferase (GAMT) deficiency several parameters may point towards the diagnosis of GAMT deficiency. These include the low levels of creatine and creatinine in urine, the high concentration of guanidinoacetic acid (GAA) in urine and the low levels of creatine and creatinine in the cerebrospinal fluid (CSF). In this study, body fluids from 10 GAMT deficient patients were analysed using (1)H NMR spectroscopy. The urine 1D (1)H NMR spectra of all the patients showed a doublet resonance at 3.98 ppm (pH 2.50) derived from GAA present in high concentration. For this compound, a good recovery and good correlation was found between an LC-MS/MS method and (1)H NMR spectroscopy. In CSF NMR spectra of these patients, the singlet resonances of creatine and creatinine (3.05 and 3.13 ppm, respectively) were absent (normally always present in (1)H NMR spectra of CSF). Due to overlap by other resonances, the doublet of GAA could not be observed. Our data demonstrate that (1)H NMR spectroscopy of urine and CSF can be used to diagnose patients with GAMT deficiency. PMID:19288536

  19. Interactions of hydrogen with alkali promoted Ru/SiO{sub 2} catalysts: A proton NMR study

    SciTech Connect

    Ozbay, U.D.

    1994-05-10

    Role of H spillover to the silica support was studied using chemisorption; a strongly bound component of spilled over H was found in the silica support which interfered with accurate measurements of active metal sites via volumetric strong H chemisorption. The volumetric chemisorption technique was modified so that measurement times were reduced from 12--36 h to 1 h. The active Ru surface was characterized means of changes in proton spin counts and NMR Knight shifts vs alkali loading. Na, K blocked the active surface of Ru metal, but Cs was pushed off by H chemisorption. The alkali promoters restricted H mobility on both metal surface and at the metal support interfaces; this is consistent with effects on Fischer-Tropsch synthesis. {sup 1}H NMR was used to study the effect of the active metal and promoter on support hydroxyl groups. The OH group density in the silica support decreased with metal and/or promoter loading, but not on a one-to-one basis; the exchange efficiency of the hydroxyls decreased with atomic size of the alkali metal. An additional downfield proton resonance was detected which was assigned to the alkali hydroxide species in the support.

  20. Transient characteristics for proton gating in laterally coupled indium-zinc-oxide transistors.

    PubMed

    Liu, Ning; Zhu, Li Qiang; Xiao, Hui; Wan, Chang Jin; Liu, Yang Hui; Chao, Jin Yu

    2015-03-25

    The control and detection over processing, transport and delivery of chemical species is of great importance in sensors and biological systems. The transient characteristics of the migration of chemical species reflect the basic properties in the processings of chemical species. Here, we observed the field-configurable proton effects in a laterally coupled transistor gated by phosphorosilicate glass (PSG). The bias on the lateral gate would modulate the interplay between protons and electrons at the PSG/indium-zinc-oxide (IZO) channel interface. Due to the modulation of protons flux within the PSG films, the IZO channel current would be modified correspondingly. The characteristic time for the proton gating is estimated to be on the order of 20 ms. Such laterally coupled oxide based transistors with proton gating are promising for low-cost portable biosensors and neuromorphic system applications. PMID:25741771

  1. Molecular dynamics and information on possible sites of interaction of intramyocellular metabolites in vivo from resolved dipolar couplings in localized 1H NMR spectra

    NASA Astrophysics Data System (ADS)

    Schröder, Leif; Schmitz, Christian; Bachert, Peter

    2004-12-01

    Proton NMR resonances of the endogenous metabolites creatine and phosphocreatine ((P)Cr), taurine (Tau), and carnosine (Cs, β-alanyl- L-histidine) were studied with regard to residual dipolar couplings and molecular mobility. We present an analysis of the direct 1H- 1H interaction that provides information on motional reorientation of subgroups in these molecules in vivo. For this purpose, localized 1H NMR experiments were performed on m. gastrocnemius of healthy volunteers using a 1.5-T clinical whole-body MR scanner. We evaluated the observable dipolar coupling strength SD0 ( S = order parameter) of the (P)Cr-methyl triplet and the Tau-methylene doublet by means of the apparent line splitting. These were compared to the dipolar coupling strength of the (P)Cr-methylene doublet. In contrast to the aliphatic protons of (P)Cr and Tau, the aromatic H2 ( δ = 8 ppm) and H4 ( δ = 7 ppm) protons of the imidazole ring of Cs exhibit second-order spectra at 1.5 T. This effect is the consequence of incomplete transition from Zeeman to Paschen-Back regime and allows a determination of SD0 from H2 and H4 of Cs as an alternative to evaluating the multiplet splitting which can be measured directly in high-resolution 1H NMR spectra. Experimental data showed striking differences in the mobility of the metabolites when the dipolar coupling constant D0 (calculated with the internuclear distance known from molecular geometry in the case of complete absence of molecular dynamics and motion) is used for comparison. The aliphatic signals involve very small order parameters S ≈ (1.4 - 3) × 10 -4 indicating rapid reorientation of the corresponding subgroups in these metabolites. In contrast, analysis of the Cs resonances yielded S ≈ (113 - 137) × 10 -4. Thus, the immobilization of the Cs imidazole ring owing to an anisotropic cellular substructure in human m. gastrocnemius is much more effective than for (P)Cr and Tau subgroups. Furthermore, 1H NMR experiments on aqueous model

  2. Analysis of Chain Branch of Polyolefins by a New Proton NMR Approach.

    PubMed

    Jung, Minhwan; Lee, Yura; Kwak, Sooyoung; Park, Heeyong; Kim, Byoungsoo; Kim, Sulhee; Lee, Kwang Hwan; Cho, Hye Sung; Hwang, Kwang Yeon

    2016-02-01

    The crystallinity of polyethylene, which significantly affects the properties of the polymer, is quite sensitive to the concentration of its branches. Thus, it is necessary to estimate branch concentration with reasonable accuracy. Currently, (13)C NMR and gel permeation chromatography-Fourier transform infrared spectroscopy are widely-used analysis methods for the analysis of branch concentration. Despite several advantages, these methods sometimes have limitations. For instance, the preparation of samples for (13)C- NMR is tedious because high-concentration samples are required and the time for analysis is greater than 12 h. To more efficiently estimate the branch concentration of polyethylene, we developed a new high-field (1)H NMR method with an improved peak resolution by employing (1) homonuclear decoupling and (2) 2D heteronuclear correlation. The new method was observed to significantly reduce the experimental time to ∼ 30 min; furthermore, sample preparation was relatively simple because the method did not require high-concentration samples. PMID:26713895

  3. High-Affinity Proton Donors Promote Proton-Coupled Electron Transfer by Samarium Diiodide.

    PubMed

    Chciuk, Tesia V; Anderson, William R; Flowers, Robert A

    2016-05-10

    The relationship between proton-donor affinity for Sm(II) ions and the reduction of two substrates (anthracene and benzyl chloride) was examined. A combination of spectroscopic, thermochemical, and kinetic studies show that only those proton donors that coordinate or chelate strongly to Sm(II) promote anthracene reduction through a PCET process. These studies demonstrate that the combination of Sm(II) ions and water does not provide a unique reagent system for formal hydrogen atom transfer to substrates. PMID:27061351

  4. Proton and carbon NMR measurements of the effects of hydration on the wheat protein ω-gliadin

    NASA Astrophysics Data System (ADS)

    Belton, P. S.; Gil, A. M.; Grant, A.; Alberti, E.; Tatham, A. S.

    1998-07-01

    The wheat protein ω-gliadin consists of a simple repeat sequence composed mainly of proline and glutamine. It thus represents a simple model for many cereal proteins and other proline and glutamine rich sequences which occur in multiple repeats. The behaviour on hydration has been examined by the measurement of proton NMR relaxation times. Sidechain motions (methyl and amino group rotation, proline ring puckering) were largely responsible for T1 relaxation. It was found that the glass transition does not affect T1 and T1 ρ relaxation and only affects transverse relaxation. Magic angle spinning experiments have been used to observe line narrowed proton spectra as well as carbon cross polarisation spectra. In the proton spectra, at high levels of hydration, backbone and sidechain NH groups are observed indicating that whole segments of the protein chain are in the mobile regime. The carbon spectra are characterised by a loss of the proline C δ signal intensity at high levels of hydration indicating the involvement of proline in the hydration process. It is concluded that the behaviour of ω-gliadin on hydration may be explained by the formation of mobile protein loops together with residual regions of strong interprotein interaction.

  5. Prospective Real Time Head Motion Correction Using Inductively Coupled Wireless NMR Probes

    PubMed Central

    Sengupta, Saikat; Tadanki, Sasidhar; Gore, John C.; Welch, E. Brian

    2014-01-01

    Purpose Head motion continues to be a major source of artifacts and data quality degradation in MRI. The goal of this work was to develop and demonstrate a novel technique for prospective, 6 degrees of freedom (6DOF) rigid body motion estimation and real time motion correction using inductively coupled wireless nuclear magnetic resonance (NMR) probe markers. Methods Three wireless probes that are inductively coupled with the scanner’s RF setup serve as fiducials on the subject’s head. A 12 ms linear navigator module is interleaved with the imaging sequence for head position estimation, and scan geometry is updated in real time for motion compensation. Flip angle amplification in the markers allows the use of extremely small navigator flip angles (~1°). A novel algorithm is presented to identify marker positions in the absence of marker specific receive channels. The method is demonstrated for motion correction in 1 mm3 gradient recalled echo experiments in phantoms and humans. Results Significant improvement of image quality is demonstrated in phantoms and human volunteers under different motion conditions. Conclusion A novel real time 6 DOF head motion correction technique based on wireless NMR probes is demonstrated in high resolution imaging at 7 Tesla. PMID:24243810

  6. Visualizing the kinetic power stroke that drives proton-coupled Zn(II) transport

    PubMed Central

    Gupta, Sayan; Chai, Jin; Cheng, Jie; D'Mello, Rhijuta; Chance, Mark R.; Fu, Dax

    2014-01-01

    The proton gradient is a principal energy source for respiration-dependent active transport, but the structural mechanisms of proton-coupled transport processes are poorly understood. YiiP is a proton-coupled zinc transporter found in the cytoplasmic membrane of E. coli, and the transport-site of YiiP receives protons from water molecules that gain access to its hydrophobic environment and transduces the energy of an inward proton gradient to drive Zn(II) efflux1,2. This membrane protein is a well characterized member3-7 of the protein family of cation diffusion facilitators (CDFs) that occurs at all phylogenetic levels8-10. X-ray mediated hydroxyl radical labeling of YiiP and mass spectrometric analysis showed that Zn(II) binding triggered a highly localized, all-or-none change of water accessibility to the transport-site and an adjacent hydrophobic gate. Millisecond time-resolved dynamics revealed a concerted and reciprocal pattern of accessibility changes along a transmembrane helix, suggesting a rigid-body helical reorientation linked to Zn(II) binding that triggers the closing of the hydrophobic gate. The gated water access to the transport-site enables a stationary proton gradient to facilitate the conversion of zinc binding energy to the kinetic power stroke of a vectorial zinc transport. The kinetic details provide energetic insights into a proton-coupled active transport reaction. PMID:25043033

  7. Role of pendant proton relays and proton-coupled electron transfer on the hydrogen evolution reaction by nickel hangman porphyrins

    PubMed Central

    Bediako, D. Kwabena; Solis, Brian H.; Dogutan, Dilek K.; Roubelakis, Manolis M.; Maher, Andrew G.; Lee, Chang Hoon; Chambers, Matthew B.; Hammes-Schiffer, Sharon; Nocera, Daniel G.

    2014-01-01

    The hangman motif provides mechanistic insights into the role of pendant proton relays in governing proton-coupled electron transfer (PCET) involved in the hydrogen evolution reaction (HER). We now show improved HER activity of Ni compared with Co hangman porphyrins. Cyclic voltammogram data and simulations, together with computational studies using density functional theory, implicate a shift in electrokinetic zone between Co and Ni hangman porphyrins due to a change in the PCET mechanism. Unlike the Co hangman porphyrin, the Ni hangman porphyrin does not require reduction to the formally metal(0) species before protonation by weak acids in acetonitrile. We conclude that protonation likely occurs at the Ni(I) state followed by reduction, in a stepwise proton transfer–electron transfer pathway. Spectroelectrochemical and computational studies reveal that upon reduction of the Ni(II) compound, the first electron is transferred to a metal-based orbital, whereas the second electron is transferred to a molecular orbital on the porphyrin ring. PMID:25298534

  8. Biosynthesis and NMR analysis of a 73-residue domain of a Saccharomyces cerevisiae G protein-coupled receptor.

    PubMed

    Estephan, Racha; Englander, Jacqueline; Arshava, Boris; Samples, Karen L; Becker, Jeffrey M; Naider, Fred

    2005-09-01

    The yeast Saccharomyces cerevisiae alpha-factor pheromone receptor (Ste2p) was used as a model G protein-coupled receptor (GPCR). A 73-mer multidomain fragment of Ste2p (residues 267-339) containing the third extracellular loop, the seventh transmembrane domain, and 40 residues of the cytosolic tail (E3-M7-24-T40) was biosynthesized fused to a carrier protein. The multidomain fusion protein (designated M7FP) was purified to near homogeneity as judged by HPLC and characterized by mass spectrometry. In minimal medium, 30-40 mg of M7FP were obtained per liter of culture. The 73-residue peptide was released from its carrier by CNBr and obtained in wild-type, (15)N, and (13)C/(15)N forms. The E3-M7-24-T40 peptide integrated into 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] and dodecylphosphocholine micelles at concentrations (200-500 microM) suitable for NMR investigations. HSQC experiments performed in organic solvents and detergent micelles on (15)N-labeled E3-M7-24-T40 showed a clear dispersion of the nitrogen-amide proton correlation cross-peaks indicative of a pure, uniformly labeled molecule that assumed a partially ordered structure. NOE connectivities, chemical shift indices, J-coupling analysis, and structural modeling suggested that in trifluoroethanol/water (1:1) helical subdomains existed in both the transmembrane and cytoslic tail of the multidomain peptide. Similar conclusions were reached in chloroform/methanol/water (4:4:1). As the cytosolic tail participates in down-regulation of Ste2p, the helical regions in the Ste2p tail may play a role in protein-protein interactions involved in endocytosis. PMID:16128581

  9. Kohn-Sham calculations of NMR shifts for paramagnetic 3d metal complexes: protocols, delocalization error, and the curious amide proton shifts of a high-spin iron(ii) macrocycle complex.

    PubMed

    Martin, Bob; Autschbach, Jochen

    2016-08-01

    A theory for the nuclear chemical shifts of molecules in arbitrary spin states is applied to a set of paramagnetic organometallic complexes of 3d metals. Ligand chemical shifts are calculated and analyzed using Kohn-Sham (KS) density functional theory with and without relativistic corrections. The roles of the KS delocalization error, Gaussian-type versus Slater-type basis sets, relativistic effects (scalar and spin-orbit), and zero field splitting (ZFS) are investigated. A strong functional dependence of the chemical shifts is apparent and correlated with the delocalization error. The functional dependence is between one and two orders of magnitude larger than variations of the NMR shifts due the other influences that are investigated. ZFS effects are negligible in the determination of the NMR chemical shifts of the complexes except at very low temperatures. The DFT calculated shifts agree reasonably well with experiment. A 73 ppm difference in the NMR shifts of the two protons in the amide groups of a high-spin Fe(ii) macrocycle complex arises from selective O → Fe dative bonding that only involves the transfer of β spin density, along with orbital delocalization throughout the ligand bonding framework which electronically couples the coordinating oxygen lone pair orbitals directly to the amide trans proton. PMID:26952694

  10. Mechanism of proton-coupled quinone reduction in Photosystem II

    PubMed Central

    Saito, Keisuke; Rutherford, A. William; Ishikita, Hiroshi

    2013-01-01

    Photosystem II uses light to drive water oxidation and plastoquinone (PQ) reduction. PQ reduction involves two PQ cofactors, QA and QB, working in series. QA is a one-electron carrier, whereas QB undergoes sequential reduction and protonation to form QBH2. QBH2 exchanges with PQ from the pool in the membrane. Based on the atomic coordinates of the Photosystem II crystal structure, we analyzed the proton transfer (PT) energetics adopting a quantum mechanical/molecular mechanical approach. The potential-energy profile suggests that the initial PT to QB•– occurs from the protonated, D1-His252 to QB•– via D1-Ser264. The second PT is likely to occur from D1-His215 to QBH− via an H-bond with an energy profile with a single well, resulting in the formation of QBH2 and the D1-His215 anion. The pathway for reprotonation of D1-His215– may involve bicarbonate, D1-Tyr246 and water in the QB site. Formate ligation to Fe2+ did not significantly affect the protonation of reduced QB, suggesting that formate inhibits QBH2 release rather than its formation. The presence of carbonate rather than bicarbonate seems unlikely because the calculations showed that this greatly perturbed the potential of the nonheme iron, stabilizing the Fe3+ state in the presence of QB•–, a situation not encountered experimentally. H-bonding from D1-Tyr246 and D2-Tyr244 to the bicarbonate ligand of the nonheme iron contributes to the stability of the semiquinones. A detailed mechanistic model for QB reduction is presented. PMID:23277574

  11. Mechanism of proton-coupled quinone reduction in Photosystem II.

    PubMed

    Saito, Keisuke; Rutherford, A William; Ishikita, Hiroshi

    2013-01-15

    Photosystem II uses light to drive water oxidation and plastoquinone (PQ) reduction. PQ reduction involves two PQ cofactors, Q(A) and Q(B), working in series. Q(A) is a one-electron carrier, whereas Q(B) undergoes sequential reduction and protonation to form Q(B)H(2). Q(B)H(2) exchanges with PQ from the pool in the membrane. Based on the atomic coordinates of the Photosystem II crystal structure, we analyzed the proton transfer (PT) energetics adopting a quantum mechanical/molecular mechanical approach. The potential-energy profile suggests that the initial PT to Q(B)(•-) occurs from the protonated, D1-His252 to Q(B)(•)(-) via D1-Ser264. The second PT is likely to occur from D1-His215 to Q(B)H(-) via an H-bond with an energy profile with a single well, resulting in the formation of Q(B)H(2) and the D1-His215 anion. The pathway for reprotonation of D1-His215(-) may involve bicarbonate, D1-Tyr246 and water in the Q(B) site. Formate ligation to Fe(2+) did not significantly affect the protonation of reduced Q(B), suggesting that formate inhibits Q(B)H(2) release rather than its formation. The presence of carbonate rather than bicarbonate seems unlikely because the calculations showed that this greatly perturbed the potential of the nonheme iron, stabilizing the Fe(3+) state in the presence of Q(B)(•-), a situation not encountered experimentally. H-bonding from D1-Tyr246 and D2-Tyr244 to the bicarbonate ligand of the nonheme iron contributes to the stability of the semiquinones. A detailed mechanistic model for Q(B) reduction is presented. PMID:23277574

  12. NMR J-coupling constants in cisplatin derivatives studied by molecular dynamics and relativistic DFT.

    PubMed

    Sutter, Kiplangat; Truflandier, Lionel A; Autschbach, Jochen

    2011-06-01

    Solvent effects on J((195)Pt-(15)N) one-bond nuclear spin-spin coupling constants (J(PtN)) of cisplatin [cis-diamminedichloroplatinum(II)] and three cisplatin derivatives are investigated using a combination of density functional theory (DFT) based ab initio molecular dynamics (aiMD) and all-electron relativistic DFT NMR calculations employing the two-component relativistic zeroth-order regular approximation (ZORA). Good agreement with experiment is obtained when explicit solvent molecules are considered and when the computations are performed with a hybrid functional. Spin-orbit coupling causes only small effects on J(PtN) . Key factors contributing to the magnitude of coupling constants are elucidated, with the most significant being the presence of solvent as well as the quality of the density functional and basis set combination. The solvent effects are of the same magnitude as J(PtN) calculated for gas-phase geometries. However, the trends of J(PtN) among the complexes are already present in the gas phase. Results obtained with a continuum solvent model agree quite well with the aiMD results, provided that the Pt solvent-accessible radius is carefully chosen. The aiMD results support the existence of a partial hydrogen-bond-like inverse-hydration-type interaction affording a weak (1)J(Pt⋅⋅⋅H(w)) coupling between the complexes and the coordinating water molecule. PMID:21381179

  13. Spin asymmetries for elastic proton scattering and the spin-dependent couplings of the Pomeron

    SciTech Connect

    Trueman, T. L.

    2008-03-01

    This paper serves as a report on the large amount of analysis done in conjunction with the polarized proton program at the Relavitistic Heavy Ion Collider at Brookhaven National Laboratory. This comprises elastic scattering data of protons on protons in colliding beam or fixed target mode and proton beams on carbon targets. In addition to providing a model for the energy dependence of the analyzing power of elastic scattering needed for proton polarimetry, it also provides some significant information about the spin dependence of dominant Regge poles. Most notably, the data indicate that the Pomeron has a significant spin-flip coupling. This allows the exploration of the double-spin flip asymmetry A{sub NN} for which some data over a wide energy range are now available, along with a concrete realization of a proposed Odderon search.

  14. Proton NMR study of a complex between the lac repressor headpiece and a 22 base pair symmetric lac operator

    SciTech Connect

    Lamerichs, R.M.J.N.; Boelens, R.; van der Marel, G.A.; van Boom, J.H.; Kaptein, R.; Buck, F.; Fera, B.; Rueterjans, H. )

    1989-04-04

    A complex between the lac repressor headpiece and a fully symmetric tight-binding 22 bp lac operator was studied by 2D NMR. Several 2D NOE spectra were recorded for the complex in both H{sub 2}O and {sup 2}H{sub 2}O. Many NOE cross-peaks between the headpiece and DNA could be identified, and changes in the chemical shift of the DNA protons upon complex formation were analyzed. Comparison of these data with those obtained for a complex between the headpiece and a 14 bp half-operator, studied previously, shows that two headpieces form a specific complex with the 22 bp lac operator in which each headpiece binds in the same way as found for the 14 bp complex. The orientation of the recognition helix in the major groove of DNA in these complexes is opposite with respect to the dyad axis to that found for other repressors.

  15. Solid-state proton NMR of paramagnetic metal complexes: DANTE spin echoes for selective excitation in inhomogeneously broadened lines

    NASA Astrophysics Data System (ADS)

    Carnevale, Diego; Perez Linde, A. J.; Bauer, Gerald; Bodenhausen, Geoffrey

    2013-08-01

    The paramagnetic complex bis(oxazolinylphenyl)amine-Fe(III)Cl2 is investigated by means of solid-state proton NMR at 18.8 T (800 MHz) using magic-angle spinning at 65 kHz. Spin echoes that are excited and refocused by combs of rotor-synchronized pulses in the manner of 'Delays Alternating with Nutation for Tailored Excitation' (DANTE) allow one to characterize different chemical environments that severely overlap in conventional MAS spectra. Such sequences combine two apparently contradictory features: an overall bandwidth exceeding several MHz, and very selective irradiation of a few kHz within inhomogeneously broadened sidebands. The experimental hyperfine interactions correlate well with DFT calculations.

  16. Free volume of poly(perfluorosulfonic acid)/SiO 2 composite proton exchange membranes by 129Xe NMR

    NASA Astrophysics Data System (ADS)

    Utiu, Lavinia; Filipoi, Carmen; Demco, Dan E.; Zhu, Xiaomin; Vinokur, Rostislav; Conradi, Oliver; Graichen, Andreas; Blümich, Bernhard; Möller, Martin

    2011-04-01

    Poly(perfluorosulfonic acid)/silica (PFSA/SiO2) composites were investigated by 129Xe NMR spectroscopy and relaxometry. 129Xe chemical shift extrapolated to zero pressure was used for calculation of average free volume hole size. This quantity reaches a maximum at 2 wt.% SiO2 that could be correlated to the performance of composites proton exchange membrane. 129Xe longitudinal magnetization relaxation revealed a bimodal distribution of the free volume that was explained by the presence of xenon atoms in the backbone and pendant-chain domains. Thus, the free volume is heterogeneous and depends on the content of SiO2. Implications of the free volume changes for the hydrogen crossover through PFSA/SiO2 membranes are also discussed.

  17. Proton NMR characterization of isomeric sulfmyoglobins: preparation, interconversion, reactivity patterns, and structural features

    SciTech Connect

    Chatfield, M.J.; La Mar, G.N.; Kauten, R.J.

    1987-11-03

    The preparations of sulfmyoglobin (sulf-Mb) by standard procedures have been found heterogeneous by /sup 1/H NMR spectroscopy. Presented here are the results of a comprehensive study of the factors that influence the selection among the three dominant isomeric forms of sperm whale sulf-Mb and their resulting detailed optical and /sup 1/H NMR properties as related to their detectability and structural properties of the heme pocket. A single isomer is formed initially in the deoxy state; further treatment in any desired oxidation/ligation state can yield two other major isomers. Acid catalysis and chromatography facilitate formation of a second isomer, particularly in the high-spin state. At neutral pH, a third isomer is formed by a first-order process. The processes that alter oxidation/ligation state are found to be reversible and are judged to affect only the metal center, but the three isomeric sulf-Mbs are found to exhibit significantly different ligand affinity and chemical stability. The present results allow, for the first time, a rational approach for preparing a given isomeric sulf-Mb in an optimally pure state for subsequent characterization by other techniques. While optical spectroscopy can distinguish the alkaline forms, only /sup 1/H NMR clearly distinguishes all three ferric isomers. The hyperfine shift patterns in the various oxidation/spin states of sulf-Mbs indicate relatively small structural alteration, and the proximal and distal sides of the heme suggest that peripheral electronic effects are responsible for the differentially reduced ligand affinities for the three isomeric sulf-Mbs. The first /sup 1/H NMR spectra of sulfhemoglobins are presented, which indicate a structure similar to that of the initially formed sulf-Mb isomer but also suggest the presence of a similar molecular heterogeneity as found for sulf-Mb, albiet to a smaller extent.

  18. Salt-dependent structure change and ion binding in cytochrome c studied by two-dimensional proton NMR

    SciTech Connect

    Feng, Yiqing; Englander, S.W. )

    1990-04-10

    To search for salt-dependent structure changes that might help to explain physicochemical differences observed in previous solution studies, two-dimensional proton NMR spectra of reduced and oxidized cytochrome c were recorded at relatively high and low salt concentrations. The results rule out substantial ionic strength dependent structure change in either redox form over the salt concentrations tested. Chemical shift changes were found for several residues within a limited segment of the oxidized protein, most prominently in the sequence Lys-86, Lys-87, Lys-88, Thr-89. A salt-dependent binding of phosphate anion(s) at this site, as observed earlier by others, is indicated. The binding of one or two phosphates at the cytochrome c surface can explain earlier small-angle X-ray scattering observations of an increase in the calculated radius of gyration of the oxidized protein at the same low-salt condition used here. The results obtained support the view that the absence of sizeable redox-dependent structure change observed in X-ray and NMR studies at varying salt conditions is characteristic of the protein at all salt conditions above the low millimolar range. Physicochemical differences between oxidized and reduced cytochrome c apparently represent differences in stability without patent structure change.

  19. Proton nuclear magnetic resonance spectroscopy (NMR) methods for determining the purity of reference drug standards and illicit forensic drug seizures.

    PubMed

    Hays, Patrick A

    2005-11-01

    A rapid, sensitive, accurate, precise, reproducible, and versatile method for determining the purity of reference drug standards and the routine analysis of illicit drugs and adulterants using proton (1H) Nuclear Magnetic Resonance (NMR) Spectroscopy is presented. The methodology uses a weighed sample dissolved in a deuterated solvent or solvent mixture containing a high purity internal standard. The NMR experiment employs 8 scans using a 45 second delay and 90 degrees pulse. In the determination of purity of reference standards, the number of quantitative determinations available is equal to the number of peak groups that are baseline resolved. The relative standard deviation (RSD) of these signals is usually < 1% for pure standards, and the results agree well with other purity determining methods. This method can also aid in the determination of correct molecular weight for standards containing an unknown number of waters of hydration or an unknown number of acids per drug in salts. Because the molar response for the hydrogen nucleus is 1 for all compounds, and since no separation media are used, only one linearity study is required to test a probe. In the presented study, the linearity of the NMR probe was determined using methamphetamine HCl dissolved in deuterium oxide (D2O) with maleic acid as the internal standard (5 mg) for a range of concentrations from 0.033 to 69.18 mg/ml with a resulting correlation coefficient of >0.9999 for all 6 methamphetamine peak groups. The spectra of complex illicit heroin, methamphetamine, MDMA, and cocaine samples are presented, as well as an extensive list of compounds, their solubilities and the solvent(s) and internal standard used. PMID:16382828

  20. Investigating the Dissolution Performance of Amorphous Solid Dispersions Using Magnetic Resonance Imaging and Proton NMR.

    PubMed

    Tres, Francesco; Coombes, Steven R; Phillips, Andrew R; Hughes, Leslie P; Wren, Stephen A C; Aylott, Jonathan W; Burley, Jonathan C

    2015-01-01

    We have investigated the dissolution performance of amorphous solid dispersions of poorly water-soluble bicalutamide in a Kollidon VA64 polymeric matrix as a function of the drug loading (5% vs. 30% bicalutamide). A combined suite of state-of-the-art analytical techniques were employed to obtain a clear picture of the drug release, including an integrated magnetic resonance imaging UV-Vis flow cell system and 1H-NMR. Off-line 1H-NMR was used for the first time to simultaneously measure the dissolution profiles and rates of both the drug and the polymer from a solid dispersion. MRI and 1H-NMR data showed that the 5% drug loading compact erodes linearly, and that bicalutamide and Kollidon VA64 are released at approximately the same rate from the molecular dispersion. For the 30% extrudate, data indicated a slower water ingress into the compact which corresponds to a slower dissolution rate of both bicalutamide and Kollidon VA64. PMID:26378506

  1. Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE

    PubMed Central

    Wisedchaisri, Goragot; Park, Min-Sun; Iadanza, Matthew G.; Zheng, Hongjin; Gonen, Tamir

    2014-01-01

    The major facilitator superfamily (MFS) is the largest collection of structurally related membrane proteins that transport a wide array of substrates. The proton-coupled sugar transporter XylE is the first member of the MFS that has been structurally characterized in multiple transporting conformations, including both the outward and inward-facing states. Here we report the crystal structure of XylE in a new inward-facing open conformation, allowing us to visualize the rocker-switch movement of the N-domain against the C-domain during the transport cycle. Using molecular dynamics simulation, and functional transport assays, we describe the movement of XylE that facilitates sugar translocation across a lipid membrane and identify the likely candidate proton-coupling residues as the conserved Asp27 and Arg133. This study addresses the structural basis for proton-coupled substrate transport and release mechanism for the sugar porter family of proteins. PMID:25088546

  2. Proton and tritium NMR relaxation studies of peptide inhibitor binding to bacterial collagenase: Conformation and dynamics

    SciTech Connect

    Dive, V.; Lai, A.; Valensin, G.; Saba, G.; Yiotakis, A.; Toma, F. )

    1991-02-15

    The interaction of succinyl-Pro-Ala, a competitive inhibitor of Achromobacter iophagus collagenase, with the enzyme was studied by longitudinal proton and tritium relaxation. Specific deuterium and tritium labeling of the succinyl part at vicinal positions allowed the measurement of the cross-relaxation rates of individual proton or tritium spin pairs in the inhibitor-enzyme complex as well as in the free inhibitor. Overall correlation times, internuclear distances, and qualitative information on the internal mobility in Suc1 (as provided by the generalized order parameter S2) could be deduced by the comparison of proton and tritium cross-relaxation of spin pairs at complementary positions in the -CH2- CH2- moiety as analyzed in terms of the model-free approach by Lipari and Szabo. The conformational and motional parameters of the inhibitor in the free and enzyme-bound state were directly compared by this method. The measurement of proton cross-relaxation in the Ala residue provided additional information on the inhibitor binding. The determination of the order parameter in different parts of the inhibitor molecule in the bound state indicates that the succinyl and alanyl residues are primarily involved in the interaction with the enzyme activity site. The succinyl moiety, characterized in solution by the conformational equilibrium among the three staggered rotamers--i.e., trans: 50%; g+: 20%; g-: 30%--adopted in the bound state the unique trans conformation.

  3. Orientational landscapes of peptides in membranes: prediction of (2)H NMR couplings in a dynamic context.

    PubMed

    Esteban-Martín, Santi; Giménez, Diana; Fuertes, Gustavo; Salgado, Jesús

    2009-12-01

    Unlike soluble proteins, membrane polypeptides face an anisotropic milieu. This imposes restraints on their orientation and provides a reference that makes structure prediction tractable by minimalistic thermodynamic models. Here we use this framework to build orientational distributions of monomeric membrane-bound peptides and to predict their expected solid-state (2)H NMR quadrupolar couplings when labeled at specific side chain positions. Using a complete rigid-body sampling of configurations relative to an implicit lipid membrane, peptide free energy landscapes are calculated. This allows us to obtain probability distributions of the peptide tilt, azimuthal rotation, and depth of membrane insertion. The orientational distributions are broad and originate from an interplay among the three relevant rigid-body degrees of freedom, which allows population of multiple states in shallow free energy minima. Remarkably, only when the orientational distributions are taken into account do we obtain a close correlation between predicted (2)H NMR splittings and values measured in experiments. Such a good correlation is not seen with splittings calculated from single configurations, being either the averaged or the lowest free energy state, showing there are distributions, rather than single structures, that best define the peptide-membrane systems. Moreover, we propose that these distributions contribute to the understanding of the rigid-body dynamics of the system. PMID:19860438

  4. Cross polarization and magic angle sample spinning NMR spectra of model organic compounds. 1. Highly protonated molecules

    SciTech Connect

    Alemany, L.B.; Grant, D.M.; Pugmire, R.J.; Alger, T.D.; Zilm, K.W.

    1983-04-20

    CP/MAS /sup 13/C NMR spectra were obtained at various contact times on ten solid organic compounds containing a variety of simple functional groups. The spectra show that signal intensities that agree with atomic ratios can be obtained with a contact time of 2.25 ms and often with a contact time as short as about 1 ms. Computer analysis of signal intensities obtained at a minimum of ten different contact times provides T/sub CH/ data that are consistent with these experimental results. The experimental results are also consistent with the previously reported lack of significant variation in the spectra of complex organic solids obtained with contact times of about 1 to 3 ms. In general, nonprotonated carbon atoms polarize more slowly than protonated carbon atoms. The compounds exhibit a wide range of proton spin lattice relaxation times. Some compounds exhibit more resonances than are found in the /sup 13/C(/sup 1/H) spectra of the compounds in solution because the crystalline environment removes the nominal spatial equivalence found for carbon atoms related to each other by unimolecular symmetry elements.

  5. Proton Dynamics on Goethite Nanoparticles and Coupling to Electron Transport.

    PubMed

    Zarzycki, Piotr; Smith, Dayle M; Rosso, Kevin M

    2015-04-14

    The surface chemistry of metal oxide particles is governed by the charge that develops at the interface with aqueous solution. Mineral transformation, biogeochemical reactions, remediation, and sorption dynamics are profoundly affected in response. Here we report implementation of replica-exchange constant-pH molecular dynamics simulations that use classical molecular dynamics for exploring configurational space and Metropolis Monte Carlo walking through protonation space with a simulated annealing escape route from metastable configurations. By examining the archetypal metal oxide, goethite (α-FeOOH), we find that electrostatic potential gradients spontaneously arise between intersecting low-index crystal faces and across explicitly treated oxide nanoparticles at a magnitude exceeding the Johnson-Nyquist voltage fluctuation. Fluctuations in adsorbed proton density continuously repolarize the surface potential bias between edge-sharing crystal faces, at a rate slower than the reported electron-polaron hopping rate in goethite interiors. This suggests that these spontaneous surface potential fluctuations will control the net movement of charge carriers in the lattice. PMID:26574382

  6. Composite alignment media for the measurement of independent sets of NMR residual dipolar couplings.

    PubMed

    Ruan, Ke; Tolman, Joel R

    2005-11-01

    The measurement of independent sets of NMR residual dipolar couplings (RDCs) in multiple alignment media can provide a detailed view of biomolecular structure and dynamics, yet remains experimentally challenging. It is demonstrated here that independent sets of RDCs can be measured for ubiquitin using just a single alignment medium composed of aligned bacteriophage Pf1 particles embedded in a strained polyacrylamide gel matrix. Using this composite medium, molecular alignment can be modulated by varying the angle between the directors of ordering for the Pf1 and strained gel matrix, or by varying the ionic strength or concentration of the Pf1 particles. This approach offers significant advantages in that greater experimental control can be exercised over the acquisition of multi-alignment RDC data while a homogeneous chemical environment is maintained across all of the measured RDC data. PMID:16248635

  7. Coupled effect of salt and pH on proteins probed with NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kukic, Predrag; O'Meara, Fergal; Hewage, Chandralal; Erik Nielsen, Jens

    2013-07-01

    The coupled effect of ionic strength (50-400 mM) and pH (2-8) on ionization and conformation equilibria of lysozyme was studied using NMR spectroscopy. Observed changes in pKa values of the ionizable groups were found to originate from perturbations in the geometry of hydrogen bonds rather than screening of electric fields. Moreover, at the ionic strengths used here, salt-induced local conformational changes had a dominant effect on chemical shifts measured on 1HN and 15N amide nuclei. Accurate modeling of these localized perturbations in structure-based energy calculations is a necessary prerequisite on the way to complete understanding of any salt-induced processes in proteins.

  8. Studies of Zinc Oxide Nanocrystals: Quantification of Capping Ligands and the Coupling of Protons and Electrons

    NASA Astrophysics Data System (ADS)

    Valdez, Carolyn N.

    The energetics of semiconductors are widely relevant to technologies ranging from chemical- and photo-catalysis to charge injection in photovoltaic materials. In these processes involving electron transfer, protons often play a critical but overlooked role in facilitating charge transfer. For example, the conduction band energies of most metal oxides in contact with an aqueous solution demonstrate a Nernstian pH dependence, an observation that cannot be explained by surface protonation models. Given that a Nernstian dependence is typically attributed to proton coupled electron transfer (PCET), we are interested in determining if the reduction of metal oxides can also be described by PCET. Zinc oxide (ZnO) nanocrystals (NCs) were chosen as a model system given the broad range of previous research on bulk and nanocrystalline forms of ZnO, the relative ease of synthesis and characterization, and their use in developing a fundamental understanding of interfacial electron transfer. We demonstrate that photochemically reduced NCs react with hydrogen-atom acceptors, indicating that both electrons and protons are transferred by the NCs. To isolate the influence of a proton coupled to the extra electron in the conduction band, the NCs have also been reduced chemically. Addition of an excess of the one-electron reductant CoCp*2 (Cp* = pentamethylcyclopentadienyl, -1.94 V vs. Fc/Fc+) gives NCs that contain extra electrons in the conduction band, without protons that arise from photoreduction. Protons can also be individually added stoichiometrically to the NCs by either a photoreduction/oxidation sequence or by addition of acid. Using these methods, we have shown that the presence of one extra proton drastically alters the redox potential of the NCs. With the addition of acid the NC orbitals are lowered, allowing the systematic variation of driving force for electron transfer from the reductant to the NCs. In the presence of excess reductant and acid, the number of electrons

  9. Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection

    SciTech Connect

    Qu, Yi; Feng, Ju; Deng, Shuang; Cao, Li; Zhang, Qibin; Zhao, Rui; Zhang, Zhaorui; Jiang, Yuxuan; Zink, Erika M.; Baker, Scott E.; Lipton, Mary S.; Pasa-Tolic, Ljiljana; Hu, Jian Z.; Wu, Si

    2014-11-19

    Protein glycosylation, an important and complex post-translational modification (PTM), is involved in various biological processes including the receptor-ligand and cell-cell interaction, and plays a crucial role in many biological functions. However, little is known about the glycan structures of important biological complex samples, and the conventional glycan enrichment strategy (i.e., size-exclusion column [SEC] separation,) prior to nuclear magnetic resonance (NMR) detection is time-consuming and tedious. In this study, we employed SEC, Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC), and ZIC-HILIC coupled with dialysis strategies to enrich the glycopeptides from the pronase E digests of RNase B, followed by NMR analysis of the glycoconjugate. Our results suggest that the ZIC-HILIC enrichment coupled with dialysis is the most efficient, which was thus applied to the analysis of biological complex sample, the pronase E digest of the secreted proteins from the fungi Aspergillus niger. The NMR spectra revealed that the secreted proteins from A. niger contain both N-linked glycans with a high-mannose core and O-linked glycans bearing mannose and glucose with 1->3 and 1->6 linkages. In all, our study provides compelling evidence that ZIC-HILIC separation coupled to dialysis is superior to the commonly used SEC separation to prepare glycopeptides for the downstream NMR analysis, which could greatly facilitate the future NMR-based glycoproteomics research.

  10. Complex dynamics of 1.3.5-trimethylbenzene-2.4.6-D3 studied by proton spin-lattice NMR relaxation and second moment of NMR line

    NASA Astrophysics Data System (ADS)

    Hołderna-Natkaniec, K.; Latanowicz, L.; Medycki, W.; Świergiel, J.; Natkaniec, I.

    2015-02-01

    Molecular dynamics of a solid 1.3.5-trimethylbenzene-2.4.6-D3 in phase I is studied on the basis of the proton T1 (24.7 MHz and 15 MHz) relaxation time measurements and the proton second moment of NMR line, M2. The measurements of the T1 were performed for temperatures from 20 to 167 K, while those of the second moment M2 from 23 to 220 K. The phase I was accurately prepared. The obtained second moment, M2 values were correlated with those based on T1 relaxation time measurements. The proton spin pairs of the methyl groups perform a complex motion being a resultant of two components characterized by the correlation times τ3T and τ3H, referring to the tunneling and over the barrier jumps in a triple potential. For τ3H the Arrhenius temperature dependence was assumed, while for τ3T - the Schrödinger one. The jumps over the barrier causes a minimum in T1 (24.7 MHz) at temperature about 35 K. The high temperatures slope of this minimum permits evaluation of the activation energy as EH=2.0 kJ/mol. The relaxation time T1 is temperature independent in the lowest temperature regime. This indicates that tunnelling correlation time assumes a constant value of about 1.3·10-10 s according to the Schrödinger equation (τ3T ≈ τ03T e B√{EH } at lowest temperatures). The tunneling jumps of methyl protons reduce M2 from the rigid lattice value 22.6 G2 to the value 5.7 G2 at zero Kelvin temperature. The second reduction to the value 1.41 G2 at 4.5-7 K is due to C3 jumps over the barrier. According to the Schrödinger equation the tunnelling jumps ceases above Ttun temperature where the thermal energy is equal to the activation energy. The Ttun equals 43.8 K (from T1 data fit, EH=2.0 kJ/mol) or 35 K (from M2 data fit, EH=1.47 kJ/mol). The second moment assumes again the value 5.7 G2 above Ttun temperature. The tunneling splitting, ωT, was estimated equal 2.47 GHz as best fit parameter from the T1 fit. The symmetrical T1 minimum indicates the same value of ωT for the all

  11. Proton NMR spectral study of UV treated live Escherichia coli Bacteria

    NASA Astrophysics Data System (ADS)

    Sorokopud, Michael

    The lethal effects of ultraviolet radiation on microorganisms have been known and utilized for many years. In sufficiently high photon fluences, light and in particular, UV light, is an effective and subtle means of killing or at least immobilizing most, if not all cells and micro-organisms. Because of their small size, light can penetrate the enclosing protective walls and enter the inner volumes where it can break organic bonds in components that are vital to cell function. Despite the fact that a very low dose of UV light (1-9 mJ/cm2) has been shown to inactivate many micro-organisms, there remains a dearth of biological information about light induced effects in molecules and their interactions within living microbial systems. The use of 1H NMR as a spectroscopic tool was chosen to undertake an examination of the possible effects resulting from exposing E. coli to lethal fluencies of UV radiation. Once sample preparation, treatment, and NMR mounting methods were optimized, the high sensitivity and high resolution capabilities of the method produced reproducible results for a series of experiments. These results reveal significant changes in the ratio of the 1H NMR spectra of the treated to untreated E.coli samples when the treated sample was exposed to a lethal fluence of 275nm light. Photons at the 275nm wavelength, used in this study, have enough energy to break all of the principle bonds in an organic molecule. The difference spectrum between treated to untreated samples appears to be fitted well using specific component spectra from these groups of compounds. Increases in NMR peak amplitudes are observed and appear to be correlated with the spectral locations of several amino acids, membrane components and several sugars/saccharides. Increases in peak intensities of 4-8% were observed in the 0.8-1.1 ppm chemical shift region, characteristic of lipid and amino acid groups. A 3.5-4% increase was observed in the 2 ppm and 3.4-4 ppm region characteristic of

  12. Probing Nonadiabaticity in the Proton-Coupled Electron Transfer Reaction Catalyzed by Soybean Lipoxygenase

    PubMed Central

    2014-01-01

    Proton-coupled electron transfer (PCET) plays a vital role in many biological and chemical processes. PCET rate constant expressions are available for various well-defined regimes, and determining which expression is appropriate for a given system is essential for reliable modeling. Quantitative diagnostics have been devised to characterize the vibronic nonadiabaticity between the electron–proton quantum subsystem and the classical nuclei, as well as the electron–proton nonadiabaticity between the electrons and proton(s) within the quantum subsystem. Herein these diagnostics are applied to a model of the active site of the enzyme soybean lipoxygenase, which catalyzes a PCET reaction that exhibits unusually high deuterium kinetic isotope effects at room temperature. Both semiclassical and electronic charge density diagnostics illustrate vibronic and electron–proton nonadiabaticity for this PCET reaction, supporting the use of the Golden rule nonadiabatic rate constant expression with a specific form of the vibronic coupling. This type of characterization will be useful for theoretical modeling of a broad range of PCET processes. PMID:25258676

  13. Thermochemistry of Proton-Coupled Electron Transfer Reagents and its Implications

    SciTech Connect

    Warren, Jeffrey J.; Tronic, Tristan A.; Mayer, James M.

    2010-12-08

    Many, if not most, redox reactions are coupled to proton transfers. This includes most common sources of chemical potential energy, from the bioenergetic processes that power cells to the fossil fuel combustion that powers cars. These proton-coupled electron transfer or PCET processes may involve multiple electrons and multiple protons, as in the 4 e–, 4 H+ reduction of dioxygen (O2) to water (eq 1), or can involve one electron and one proton such as the formation of tyrosyl radicals from tyrosine residues (TyrOH) in enzymatic catalytic cycles (eq 2). In addition, many multi-electron, multi-proton processes proceed in one-electron and one-proton steps. Organic reactions that proceed in one-electron steps involve radical intermediates, which play critical roles in a wide range of chemical, biological, and industrial processes. This broad and diverse class of PCET reactions are central to a great many chemical and biochemical processes, from biological catalysis and energy transduction, to bulk industrial chemical processes, to new approaches to solar energy conversion. PCET is therefore of broad and increasing interest, as illustrated by this issue and a number of other recent reviews.

  14. Nickel phlorin intermediate formed by proton-coupled electron transfer in hydrogen evolution mechanism

    PubMed Central

    Solis, Brian H.; Maher, Andrew G.; Dogutan, Dilek K.; Nocera, Daniel G.; Hammes-Schiffer, Sharon

    2016-01-01

    The development of more effective energy conversion processes is critical for global energy sustainability. The design of molecular electrocatalysts for the hydrogen evolution reaction is an important component of these efforts. Proton-coupled electron transfer (PCET) reactions, in which electron transfer is coupled to proton transfer, play an important role in these processes and can be enhanced by incorporating proton relays into the molecular electrocatalysts. Herein nickel porphyrin electrocatalysts with and without an internal proton relay are investigated to elucidate the hydrogen evolution mechanisms and thereby enable the design of more effective catalysts. Density functional theory calculations indicate that electrochemical reduction leads to dearomatization of the porphyrin conjugated system, thereby favoring protonation at the meso carbon of the porphyrin ring to produce a phlorin intermediate. A key step in the proposed mechanisms is a thermodynamically favorable PCET reaction composed of intramolecular electron transfer from the nickel to the porphyrin and proton transfer from a carboxylic acid hanging group or an external acid to the meso carbon of the porphyrin. The C–H bond of the active phlorin acts similarly to the more traditional metal-hydride by reacting with acid to produce H2. Support for the theoretically predicted mechanism is provided by the agreement between simulated and experimental cyclic voltammograms in weak and strong acid and by the detection of a phlorin intermediate through spectroelectrochemical measurements. These results suggest that phlorin species have the potential to perform unique chemistry that could prove useful in designing more effective electrocatalysts. PMID:26655344

  15. Transverse Mode-Coupling Instability in the CERN Super Proton Synchrotron

    NASA Astrophysics Data System (ADS)

    Métral, E.; Arduini, G.; Benedetto, E.; Burkhardt, H.; Shaposhnikova, E.; Rumolo, G.

    2005-06-01

    A vertical single-bunch instability has been observed in 2003 right after injection at 26 GeV/c in the CERN Super Proton Synchrotron (SPS). High-intensity proton bunches (˜1.2 1011 p/b) with low longitudinal emittance (˜0.2 eVs) are affected by heavy losses after less than one synchrotron period. Such phenomenon has already been observed with leptons in many machines, e.g. in the SPS, or with protons at transition, e.g. in the CERN Proton Synchrotron (PS). However, to the authors' knowledge, it is the first time with protons far from transition. The absence of transverse mode-coupling instability in hadron machines is generally explained by three mechanisms: (i) the intensity threshold for the longitudinal microwave instability is generally lower than for the transverse mode-coupling instability, (ii) the intensity threshold due to mode-coupling between the two lowest azimuthal modes increases with space charge, and (iii) the intensity threshold increases with bunch length (in the long-bunch regime). In this talk measurements performed in the SPS are compared to analytical and simulation predictions.

  16. Modulation of Proton-Coupled Electron Transfer through Molybdenum-Quinonoid Interactions.

    PubMed

    Henthorn, Justin T; Agapie, Theodor

    2016-06-01

    An expanded series of π-bound molybdenum-quinonoid complexes supported by pendant phosphines has been synthesized. These compounds formally span three protonation-oxidation states of the quinonoid fragment (catechol, semiquinone, quinone) and two different oxidation states of the metal (Mo(0), Mo(II)), notably demonstrating a total of two protons and four electrons accessible in the system. Previously, the reduced Mo(0)-catechol complex 1 and its reaction with dioxygen to yield the two-proton/two-electron oxidized Mo(0)-quinone compound 4 was explored, while, herein, the expansion of the series to include the two-electron oxidized Mo(II)-catechol complex 2, the one-proton/two-electron oxidized Mo-semiquinone complex 3, and the two-proton/four-electron oxidized Mo(II)-quinone complexes 5 and 6 is reported. Transfer of multiple equivalents of protons and electrons from the Mo(0) and Mo(II) catechol complexes, 1 and 2, to H atom acceptor TEMPO suggests the presence of weak O-H bonds. Although thermochemical analyses are hindered by the irreversibility of the electrochemistry of the present compounds, the reactivity observed suggests weaker O-H bonds compared to the free catechol, indicating that proton-coupled electron transfer can be facilitated significantly by the π-bound metal center. PMID:27227812

  17. Thermochemistry of Proton-Coupled Electron Transfer Reagents and its Implications

    SciTech Connect

    Warren, Jeffrey J; Tronic, Tristan A; Mayer, James M

    2010-01-01

    The primary goals of this review are (1) to assemble thermochemical data—reduction potentials, pK{sub a} values, and bond dissociation free energies and enthalpies—from disparate sources and (2) to illustrate the utility of these data in understanding proton-coupled redox chemistry. We hope to have illustrated the value and power of thermochemical cycles (“square schemes”).

  18. The HP-1 maquette: From an apoprotein structure to a structured hemoprotein designed to promote redox-coupled proton exchange

    PubMed Central

    Huang, Steve S.; Koder, Ronald L.; Lewis, Mitchell; Wand, A. Joshua; Dutton, P. Leslie

    2004-01-01

    Synthetic heme-binding four-α-helix bundles show promise as working model systems, maquettes, for understanding heme cofactor–protein assembly and function in oxidoreductases. Despite successful inclusion of several key functional elements of natural proteins into a family of heme protein maquettes, the lack of 3D structures, due principally to conformational heterogeneity, has prevented them from achieving their full potential. We report here the design and synthesis of HP-1, a disulfide-bridged two-α-helix peptide that self-assembles to form an antiparallel twofold symmetric diheme four-α-helix bundle protein with a stable conformation on the NMR time-scale. The HP-1 design strategy began with the x-ray crystal structure of the apomaquette L31M, an apomaquette derived from the structurally heterogeneous tetraheme-binding H10H24 prototype. L31M was functionally redesigned to accommodate two hemes ligated to histidines and to retain the strong coupling of heme oxidation-reduction to glutamate acid–base transitions and proton exchange that was characterized in molten globule predecessors. Heme insertion was modeled with angular constraints statistically derived from natural proteins, and the pattern of hydrophobic and hydrophilic residues on each helix was then altered to account for this large structural reorganization. The transition to structured holomaquette involved the alteration of 6 of 31 residues in each of the four identical helices and, unlike our earlier efforts, required no design intermediates. Oxidation-reduction of both hemes displays an unusually low midpoint potential (–248 mV vs. normal hydrogen electrode at pH 9.0), which is strongly coupled to proton binding, as designed. PMID:15056758

  19. Sensitivity enhancement of remotely coupled NMR detectors using wirelessly powered parametric amplification.

    PubMed

    Qian, Chunqi; Murphy-Boesch, Joseph; Dodd, Stephen; Koretsky, Alan

    2012-09-01

    A completely wireless detection coil with an integrated parametric amplifier has been constructed to provide local amplification and transmission of MR signals. The sample coil is one element of a parametric amplifier using a zero-bias diode that mixes the weak MR signal with a strong pump signal that is obtained from an inductively coupled external loop. The NMR sample coil develops current gain via reduction in the effective coil resistance. Higher gain can be obtained by adjusting the level of the pumping power closer to the oscillation threshold, but the gain is ultimately constrained by the bandwidth requirement of MRI experiments. A feasibility study here shows that on a NaCl/D(2) O phantom, (23) Na signals with 20 dB of gain can be readily obtained with a concomitant bandwidth of 144 kHz. This gain is high enough that the integrated coil with parametric amplifier, which is coupled inductively to external loops, can provide sensitivity approaching that of direct wire connection. PMID:22246567

  20. Sensitivity Enhancement of Remotely Coupled NMR Detectors using Wirelessly Powered Parametric Amplification

    PubMed Central

    Qian, Chunqi; Murphy-Boesch, Joseph; Dodd, Stephen; Koretsky, Alan

    2011-01-01

    A completely wireless detection coil with an integrated parametric amplifier has been constructed to provide local amplification and transmission of MR signals. The sample coil is one element of a parametric amplifier using a zero-bias diode that mixes the weak MR signal with a strong pump signal that is obtained from an inductively coupled external loop. The NMR sample coil develops current gain via reduction in the effective coil resistance. Higher gain can be obtained by adjusting the level of the pumping power closer to the oscillation threshold, but the gain is ultimately constrained by the bandwidth requirement of MRI experiments. A feasibility study here shows that on a NaCl/D2O phantom, 23Na signals with 20 dB of gain can be readily obtained with a concomitant bandwidth of 144 kHz. This gain is high enough that the integrated coil with parametric amplifier, which is coupled inductively to external loops, can provide sensitivity approaching that of direct wire connection. PMID:22246567

  1. Proton NMR studies of the electronic structure of ZrH/sub x/

    NASA Technical Reports Server (NTRS)

    Attalla, A.; Bowman, R. C., Jr.; Craft, B. D.; Venturini, E. L.; Rhim, W. K.

    1982-01-01

    The proton spin lattice relaxation times and Knight shifts were measured in f.c.c. (delta-phase) and f.c.t. (epsilon-phase) ZrH/sub x/ for 1.5 or = to x or = to 2.0. Both parameters indicate that N(E/sub F/) is very dependent upon hydrogen content with a maximum occurring at ZrH1 83. This behavior is ascribed to modifications in N(E/sub F/) through a fcc/fct distortion in ZrH/sub x/ associated with a Jahn-Teller effect.

  2. Proton decoupling and recoupling under double-nutation irradiation in solid-state NMR

    SciTech Connect

    Takeda, Kazuyuki Wakisaka, Asato; Takegoshi, K.

    2014-12-14

    The effect of {sup 1}H decoupling in magic-angle spinning solid-state NMR is studied under radiofrequency irradiation causing simultaneous nutations around a pair of orthogonal axes. Double-nutation with an arbitrary pair of nutation frequencies is implemented through modulation of the amplitude, phase, and frequency of the transmitting pulses. Similarity and difference of double-nutation decoupling and two-pulse phase-modulation decoupling schemes [A. E. Bennett, C. M. Rienstra, M. Auger, K. V. Lakshmi, and R. G. Griffin, J. Chem. Phys. 103, 6951–6958 (1995) and I. Scholz, P. Hodgkinson, B. H. Meier, and M. Ernst, J. Chem. Phys. 130, 114510 (2009)] are discussed. The structure of recoupling bands caused by interference of the {sup 1}H spin nutation with sample spinning is studied by both experiments and numerical simulations.

  3. Proton decoupling and recoupling under double-nutation irradiation in solid-state NMR

    NASA Astrophysics Data System (ADS)

    Takeda, Kazuyuki; Wakisaka, Asato; Takegoshi, K.

    2014-12-01

    The effect of 1H decoupling in magic-angle spinning solid-state NMR is studied under radiofrequency irradiation causing simultaneous nutations around a pair of orthogonal axes. Double-nutation with an arbitrary pair of nutation frequencies is implemented through modulation of the amplitude, phase, and frequency of the transmitting pulses. Similarity and difference of double-nutation decoupling and two-pulse phase-modulation decoupling schemes [A. E. Bennett, C. M. Rienstra, M. Auger, K. V. Lakshmi, and R. G. Griffin, J. Chem. Phys. 103, 6951-6958 (1995) and I. Scholz, P. Hodgkinson, B. H. Meier, and M. Ernst, J. Chem. Phys. 130, 114510 (2009)] are discussed. The structure of recoupling bands caused by interference of the 1H spin nutation with sample spinning is studied by both experiments and numerical simulations.

  4. Isotope-edited proton NMR study on the structure of a pepsin/inhibitor complex

    SciTech Connect

    Fesik, S.W.; Luly, J.R.; Erickson, J.W.; Abad-Zapatero, C.

    1988-11-01

    A general approach is illustrated for providing detailed structural information on large enzyme/inhibitor complexes using NMR spectroscopy. The method involves the use of isotopically labeled ligands to simplify two-dimensional NOE spectra of large molecular complexes by isotope-editing techniques. With this approach, the backbone and side-chain conformations (at the P/sub 2/ and P/sub 3/ sites) of a tightly bound inhibitor of porcine pepsin have bene determined. In addition, structural information on the active site of pepsin has been obtained. Due to the sequence homology between porcine pepsin and human renin, this structural information may prove useful for modeling renin/inhibitor complexes with the ultimate goal of designing more effective renin inhibitors. Moreover, this general approach can be applied to study other biological systems of interest such as other enzyme/inhibitor complexes, ligands bound to soluble receptors, and enzyme/substrate interactions.

  5. The stereospecific assignment of H5' and H5' in RNA using the sign of two-bond carbon-proton scalar couplings

    SciTech Connect

    Hines, J.V.; Varani, G.; Landry, S.M.; Tinoco, I. Jr. )

    1993-11-17

    Stereospecific assignment of H5' and H5' protons in the NMR spectra of nucleic acids provides significant improvement in the use of NOE distance and torsion angle constraints for structure determination. With stereospecific assignments, the torsion angles [beta] (P5'-O5'-C5'-C4') and [gamma] (O5'-C5'-C4'-C3') can be determined on the basis of [sup 1]H-[sup 1]H and [sup 31]P-[sup 1]H couplings. In addition, stereospecific assignment allows use of NOE distance constraints for H5' and H5'. We report a novel, independent method for the stereospecific assignment of the H5' (pro-S) and H5' (pro-R) protons which is based only on the sign of the carbon-proton two-bond scalar couplings and will not be greatly limited by line width. The sign of [sup 2]J[sub CH] can also be used to determine torsion angle [gamma] and the sugar conformation. Determination of the sign of the two-bond carbon-proton couplings provides a useful new method for the structure determination of RNA molecules. The ribose sugar conformation and torsion angle [gamma] (O5'-C5'-C4'-C3') can be specified. Furthermore, H5' and H5' protons can be stereospecifically assigned, allowing their use in NOE distance constraints and in determining [beta] (P5'-O5'-C5'-C4'). The correlation we have reported between the sign of [sup 2]J[sub CH] and RNA structure will be particularly useful in the study of large RNAs and RNA-protein complexes. 21 refs., 1 fig., 1 tab.

  6. The differences in the T2 relaxation rates of the protons in the partially-deuteriated and fully protonated sugar residues in a large oligo-DNA ('NMR-window') gives complementary structural information.

    PubMed Central

    Agback, P; Maltseva, T V; Yamakage, S I; Nilson, F P; Földesi, A; Chattopadhyaya, J

    1994-01-01

    Selective incorporation of the stereospecifically deuteriated sugar moieties (> 97 atom % 2H enhancements at H2', H2'', H3' and H5'/5'' sites, approximately 85 atom % 2H enhancement at H4' and approximately 20 atom % 2H enhancement at H1') in DNA and RNA by the 'NMR-window' approach has been shown to solve the problem of the resonance overlap [refs. 1, 2 & 3]. Such specific deuterium labelling gives much improved resolution and sensitivity of the residual sugar proton (i.e. H1' or H4') vicinal to the deuteriated centers (ref. 3). The T2 relaxation time of the residual protons also increases considerably in the partially-deuteriated (shown by underline) sugar residues in dinucleotides [d(CpG), d(GpC), d(ApT), d(TpA)], trinucleotide r(A2'p5'A2'p5'A) and 20-mer DNA duplex 5'd(C1G2C3-G4C5G6C7G8A9A10T11T12C13G14C15G16C17G18C19G20)(2) 3'. The protons with shorter T2 can be filtered away using a number of different NMR experiments such as ROESY, MINSY or HAL. The NOE intensity of the cross-peaks in these experiments includes only straight pathway from H1' to aromatic proton (i-i and i-i + 1) without any spin-diffusion. The volumes of these NOE cross-peaks could be measured with high accuracy as their intensity is 3 to 4 times larger than the corresponding peaks in the fully protonated residues in the normal NOESY spectra. The structural informations thus obtainable from the residual protons in the partially-deuteriated part of the duplex and the fully protonated part in the 'NMR window' can indeed complement each other. PMID:8190632

  7. Proton NMR investigation of the heme active site structure of an engineered cytochrome c peroxidase that mimics manganese peroxidase.

    PubMed

    Wang, X; Lu, Y

    1999-07-13

    The heme active site structure of an engineered cytochrome c peroxidase [MnCcP; see Yeung, B. K., et al. (1997) Chem. Biol. 4, 215-221] that closely mimics manganese peroxidase (MnP) has been characterized by both one- and two-dimensional NMR spectroscopy. All hyperfine-shifted resonances from the heme pocket as well as resonances from catalytically relevant amino acid residues in the congested diamagnetic envelope have been assigned. From the NMR spectral assignment and the line broadening pattern of specific protons in NOESY spectra of MnCcP, the location of the engineered Mn(II) center is firmly identified. Furthermore, we found that the creation of the Mn(II)-binding site in CcP resulted in no detectable structural changes on the distal heme pocket of the protein. However, notable structural changes are observed at the proximal side of the heme cavity. Both CepsilonH shift of the proximal histidine and (15)N shift of the bound C(15)N(-) suggest a weaker heme Fe(III)-N(His) bond in MnCcP compared to WtCcP. Our results indicate that the engineered Mn(II)-binding site in CcP resulted in not only a similar Mn(II)-binding affinity and improved MnP activity, but also weakened the Fe(III)-N(His) bond strength of the template protein CcP so that its bond strength is similar to that of the target protein MnP. The results presented here help elucidate the impact of designing a metal-binding site on both the local and global structure of the enzyme, and provide a structural basis for engineering the next generation of MnCcP that mimics MnP more closely. PMID:10413489

  8. HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections.

    PubMed

    Cornilescu, Gabriel; Bahrami, Arash; Tonelli, Marco; Markley, John L; Eghbalnia, Hamid R

    2007-08-01

    We describe a novel method for the robust, rapid, and reliable determination of J couplings in multi-dimensional NMR coupling data, including small couplings from larger proteins. The method, "High-resolution Iterative Frequency Identification of Couplings" (HIFI-C) is an extension of the adaptive and intelligent data collection approach introduced earlier in HIFI-NMR. HIFI-C collects one or more optimally tilted two-dimensional (2D) planes of a 3D experiment, identifies peaks, and determines couplings with high resolution and precision. The HIFI-C approach, demonstrated here for the 3D quantitative J method, offers vital features that advance the goal of rapid and robust collection of NMR coupling data. (1) Tilted plane residual dipolar couplings (RDC) data are collected adaptively in order to offer an intelligent trade off between data collection time and accuracy. (2) Data from independent planes can provide a statistical measure of reliability for each measured coupling. (3) Fast data collection enables measurements in cases where sample stability is a limiting factor (for example in the presence of an orienting medium required for residual dipolar coupling measurements). (4) For samples that are stable, or in experiments involving relatively stronger couplings, robust data collection enables more reliable determinations of couplings in shorter time, particularly for larger biomolecules. As a proof of principle, we have applied the HIFI-C approach to the 3D quantitative J experiment to determine N-C' RDC values for three proteins ranging from 56 to 159 residues (including a homodimer with 111 residues in each subunit). A number of factors influence the robustness and speed of data collection. These factors include the size of the protein, the experimental set up, and the coupling being measured, among others. To exhibit a lower bound on robustness and the potential for time saving, the measurement of dipolar couplings for the N-C' vector represents a realistic

  9. Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer

    SciTech Connect

    Michalczyk, Ryszard; Unkefer, Clifford J.; Bacik, John -Paul; Schrader, Tobias E.; Ostermann, Andreas; Kovalevsky, Andrey Y.; McKenna, Robert; Fisher, Suzanne Zoe

    2015-05-05

    Proton transfer is a fundamental mechanism at the core of many enzyme-catalyzed reactions. It is also exquisitely sensitive to a number of factors, including pH, electrostatics, proper active-site geometry, and chemistry. Carbonic anhydrase has evolved a fast and efficient way to conduct protons through a combination of hydrophilic amino acid side chains that coordinate a highly ordered H-bonded water network. This study uses a powerful approach, combining NMR solution studies with neutron protein crystallography, to determine the effect of pH and divalent cations on key residues involved in proton transfer in human carbonic anhydrase. Lastly, the results have broad implications for our understanding of proton transfer and how subtle changes in ionization and H-bonding interactions can modulate enzyme catalysis.

  10. Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer

    DOE PAGESBeta

    Michalczyk, Ryszard; Unkefer, Clifford J.; Bacik, John -Paul; Schrader, Tobias E.; Ostermann, Andreas; Kovalevsky, Andrey Y.; McKenna, Robert; Fisher, Suzanne Zoe

    2015-05-05

    Proton transfer is a fundamental mechanism at the core of many enzyme-catalyzed reactions. It is also exquisitely sensitive to a number of factors, including pH, electrostatics, proper active-site geometry, and chemistry. Carbonic anhydrase has evolved a fast and efficient way to conduct protons through a combination of hydrophilic amino acid side chains that coordinate a highly ordered H-bonded water network. This study uses a powerful approach, combining NMR solution studies with neutron protein crystallography, to determine the effect of pH and divalent cations on key residues involved in proton transfer in human carbonic anhydrase. Lastly, the results have broad implicationsmore » for our understanding of proton transfer and how subtle changes in ionization and H-bonding interactions can modulate enzyme catalysis.« less

  11. United Atom Rotational Coupling in Proton + Helium Collision

    NASA Astrophysics Data System (ADS)

    Wang, Chiiling

    United-atom 2p(sigma)-2p(pi) rotational coupling in asymmetric collisions is influenced by an avoided crossing between the 2p(sigma) and 2s(sigma) orbitals. This influence is studied using the HeH('+) system as a prototype. In (SIGMA)(,2)-(SIGMA)(,3)-(pi)(,1) three-state calculations, the time-dependent Schrodinger equation is solved numerically. Substantial population of the 2s(sigma) state is found, which disagrees with the estimates based on the Landau-Zener model. The (SIGMA)(,3) level is populated directly by transitions near the avoided crossing at b = 0.4 au and indirectly by (SIGMA)(,2)-(pi)(,1)-(SIGMA)(,3) rotational coupling for b > 0.4 au. The ratios of P(,(SIGMA)(,3))(b)/ P(,(SIGMA)(,3))(b) + P(,(pi)(,1))(b) are calculated and compared with Dr. R. Hippler's experimental data. A six-state calculation, in the basis of (SIGMA)(,1), (SIGMA)(,2), (SIGMA)(,3), (SIGMA)(,4), (pi)(,1) and (pi)(,2) molecular states, is also made. Cross sections and alignment and orientation parameters have been computed from the transition amplitudes for various energies.

  12. H1 NMR study of proton dynamics in Cs5H3(SO4)4•xH2O

    NASA Astrophysics Data System (ADS)

    Suzuki, Koh-Ichi; Hayashi, Shigenobu

    2006-10-01

    Complicated phase relations in Cs5H3(SO4)4•xH2O are revealed by thermal analyses. A superprotonic phase transition takes place at 420K for both the hydrated and the anhydrous forms. The H1 magic-angle-spinning (MAS) NMR spectra were traced at room temperature and at Larmor frequency of 400.13MHz . The H1 chemical shifts of the acidic protons are 10.9 and 11.2ppm for the hydrated and the anhydrous forms, respectively. The hydrated sample shows a signal at 9.7ppm additionally, which is ascribed to H3O+ . Proton dynamics has been studied by H1 static NMR spectra and spin-lattice relaxation times, T1 . In both a room-temperature phase (phase RT) and a high-temperature phase (phase HT), translational diffusion of protons takes place. The H1 mean residence times in phase RT are obtained from the second moment analysis; Ea=49kJmol-1 and τ0=1.8×10-11s for the anhydrous form and Ea=31kJmol-1 and τ0=2.2×10-9s for the hydrated form. From the analysis of H1 T1 results we have obtained parameters of proton diffusion for phase HT; Ea=34kJmol-1 and τ0=3×10-13s for the anhydrous form and Ea=36kJmol-1 and τ0=3×10-14s for the hydrated form. In both phases, protons diffuse faster in the hydrated form than in the anhydrous form. The proton conductivities estimated from the NMR results for the anhydrous form agree with the macroscopic values in literature.

  13. Proton NMR study of molecular dynamics in ammonium tribromo stannate (NH 4SnBr 3)

    NASA Astrophysics Data System (ADS)

    Ramesh, K. P.; Devaraj, N.; Ramakrishna, J.; Venu, K.; Sastry, V. S. S.

    1993-11-01

    The proton second moment M2 and spin-lattice relaxation time T1 have been measured in ammonium tribromo stannate (NH 4SnBr 3) in the temperature range 77-300 K, to determine the ammonium dynamics. The continuous wave signal is strong and narrow at 77 and 300 K but has revealed an interesting intensity anomaly between 210 and 125 K. T1 shows a maximum (13 s) around 220 K. No minimum in the T1 vs 1000/ T plot was observed down to 77 K. M2 and T1 results are interpreted in terms of NH +4 ion dynamics. The activation energy Ea for NH +4 ion reorientation is estimated to be 1.4 kcal mol -1.

  14. Proton NMR analysis of octane number for motor gasoline: Part V

    SciTech Connect

    Ichikawa, M.; Nonaka, N.; Amano, H.; Takada, I.; Ishimori, S.; Andoh, H.; Kumamoto, K.

    1992-10-01

    A method to predict the octane number of automobile gasoline containing methyl tert-butyl ether (MTBE) by proton magnetic resonance (PMR) spectrometry was studied. Samples of gasoline whose octane numbers had been identified according to the ASTM standards (commercially available premium gasoline to which MTBE was added at rates of 7 vol % and 14 vol %) were used in this investigation of the effect of MTBE on the octane number. The findings were utilized to introduce a term regarding MTBE into the previously reported linear regression equation for estimating the octane number from the PMR spectrum, and the appropriateness of the linear regression equation was assessed. As a result the MTBE contents in the sample were determined with satisfactory accuracy by using a standard addition method, and a linear regression equation reflecting the effect of MTBE was obtained. These achievements are reported. 11 refs., 3 figs., 5 tabs.

  15. The coupling of electron transfer and proton translocation: electrostatic calculations on Paracoccus denitrificans cytochrome c oxidase.

    PubMed Central

    Kannt, A; Lancaster, C R; Michel, H

    1998-01-01

    We have calculated the electrostatic potential and interaction energies of ionizable groups and analyzed the response of the protein environment to redox changes in Paracoccus denitrificans cytochrome c oxidase by using a continuum dielectric model and finite difference technique. Subsequent Monte Carlo sampling of protonation states enabled us to calculate the titration curves of all protonatable groups in the enzyme complex. Inclusion of a model membrane allowed us to restrict the calculations to the functionally essential subunits I and II. Some residues were calculated to have complex titration curves, as a result of strong electrostatic coupling, desolvation, and dipolar interactions. Around the heme a3-CuB binuclear center, we have identified a cluster of 18 strongly interacting residues that account for most of the proton uptake linked to electron transfer. This was calculated to be between 0.7 and 1.1 H+ per electron, depending on the redox transition considered. A hydroxide ion bound to CuB was determined to become protonated to form water upon transfer of the first electron to the binuclear site. The bulk of the protonation changes linked to further reduction of the heme a3-CuB center was calculated to be due to proton uptake by the interacting cluster and Glu(II-78). Upon formation of the three-electron reduced state (P1), His325, modeled in an alternative orientation away from CuB, was determined to become protonated. The agreement of these results with experiment and their relevance in the light of possible mechanisms of redox-coupled proton transfer are discussed. PMID:9533684

  16. The coupling of electron transfer and proton translocation: electrostatic calculations on Paracoccus denitrificans cytochrome c oxidase.

    PubMed

    Kannt, A; Lancaster, C R; Michel, H

    1998-02-01

    We have calculated the electrostatic potential and interaction energies of ionizable groups and analyzed the response of the protein environment to redox changes in Paracoccus denitrificans cytochrome c oxidase by using a continuum dielectric model and finite difference technique. Subsequent Monte Carlo sampling of protonation states enabled us to calculate the titration curves of all protonatable groups in the enzyme complex. Inclusion of a model membrane allowed us to restrict the calculations to the functionally essential subunits I and II. Some residues were calculated to have complex titration curves, as a result of strong electrostatic coupling, desolvation, and dipolar interactions. Around the heme a3-CuB binuclear center, we have identified a cluster of 18 strongly interacting residues that account for most of the proton uptake linked to electron transfer. This was calculated to be between 0.7 and 1.1 H+ per electron, depending on the redox transition considered. A hydroxide ion bound to CuB was determined to become protonated to form water upon transfer of the first electron to the binuclear site. The bulk of the protonation changes linked to further reduction of the heme a3-CuB center was calculated to be due to proton uptake by the interacting cluster and Glu(II-78). Upon formation of the three-electron reduced state (P1), His325, modeled in an alternative orientation away from CuB, was determined to become protonated. The agreement of these results with experiment and their relevance in the light of possible mechanisms of redox-coupled proton transfer are discussed. PMID:9533684

  17. Using Pseudocontact Shifts and Residual Dipolar Couplings as Exact NMR Restraints for the Determination of Protein Structural Ensembles.

    PubMed

    Camilloni, Carlo; Vendruscolo, Michele

    2015-12-29

    Nuclear magnetic resonance (NMR) spectroscopy provides detailed information about the structure and dynamics of proteins by exploiting the conformational dependence of the magnetic properties of certain atomic nuclei. The mapping between NMR measurements and molecular structures, however, often requires approximated descriptions based on the fitting of a number of parameters, thus reducing the quality of the information available from the experiments. To improve on this limitation, we show here that it is possible to use pseudocontact shifts and residual dipolar couplings as "exact" NMR restraints. We implement this strategy by using a replica-averaging method and illustrate its application by calculating an ensemble of structures representing the dynamics of the two-domain protein calmodulin. PMID:26624789

  18. Insights into proton-coupled electron transfer mechanisms of electrocatalytic H2 oxidation and production

    PubMed Central

    Horvath, Samantha; Fernandez, Laura E.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon

    2012-01-01

    The design of molecular electrocatalysts for H2 oxidation and production is important for the development of alternative renewable energy sources that are abundant, inexpensive, and environmentally benign. Recently, nickel-based molecular electrocatalysts with pendant amines that act as proton relays for the nickel center were shown to effectively catalyze H2 oxidation and production. We developed a quantum mechanical approach for studying proton-coupled electron transfer processes in these types of molecular electrocatalysts. This theoretical approach is applied to a nickel-based catalyst in which phosphorous atoms are directly bonded to the nickel center, and nitrogen atoms of the ligand rings act as proton relays. The catalytic step of interest involves electron transfer between the nickel complex and the electrode as well as intramolecular proton transfer between the nickel and nitrogen atoms. This process can occur sequentially, with either the electron or proton transferring first, or concertedly, with the electron and proton transferring simultaneously without a stable intermediate. The electrochemical rate constants are calculated as functions of overpotential for the concerted electron-proton transfer reaction and the two electron transfer reactions in the sequential mechanisms. Our calculations illustrate that the concerted electron-proton transfer standard rate constant will increase as the equilibrium distance between the nickel and nitrogen atoms decreases and as the pendant amines become more flexible to facilitate the contraction of this distance with a lower energy penalty. This approach identifies the favored mechanisms under various experimental conditions and provides insight into the impact of substituents on the nitrogen and phosphorous atoms. PMID:22529352

  19. High-Speed Magic-Angle Spinning 13C MAS NMR Spectra of Adamantane: Self-Decoupling of the Heteronuclear Scalar Interaction and Proton Spin Diffusion

    NASA Astrophysics Data System (ADS)

    Ernst, Matthias; Verhoeven, Aswin; Meier, Beat H.

    1998-02-01

    We have investigated the carbon line shape of solid adamantane under high-speed magic-angle sample spinning (MAS) acquired without proton decoupling. The CH-group shows a spinning-speed-dependent line broadening while the CH2-group consists of a spinning-speed-independent sharp component and a spinning-speed-dependent broader part. These phenomena can be explained by self-decoupling of theJ-interaction due to proton spin diffusion. Such a self-decoupling process can be described by a magnetization exchange process between the multiplet lines. Changing the spin-diffusion rate constant by off-resonance irradiation of the protons allows us to observe the full range from slow exchange to coalescence to fast exchange of the carbon spectra. One of the multiplet components in the CH2-group corresponds to a group spin of the protons of zero and therefore does not couple to the other protons. This gives rise to the sharp central line. The magnetization exchange rate constant between the different multiplet lines can be determined from the spectra and is a measure for the spinning-speed-dependent proton spin-diffusion rate constant. Even at an MAS speed of 30 kHz, proton spin diffusion is still observable despite the relatively weak intermolecular proton dipolar-coupling network in adamantane which results in a static proton line width of only 14 kHz (full width at half height).

  20. The effects of bone on proton NMR relaxation times of surrounding liquids

    NASA Technical Reports Server (NTRS)

    Davis, C. A.; Genant, H. K.; Dunham, J. S.

    1986-01-01

    Preliminary attempts by our group at UCSF to assess fat content of vertebral marrow in the lumbar spine using relaxation time information demonstrated that the presence of trabecular bone affects relaxation times. The objective of this work was a thorough study of the effects of bone on NMR relaxation characteristics of surrounding liquids. Trabecular bone from autopsy specimens was ground up and sifted into a series of powders with graded densities ranging from 0.3 gm/cc to 0.8 gm/cc. Each powder was placed first in n-saline and then in cottonseed oil. With spectroscopy, spin-lattice relaxation times (T1) and effective spin-spin relaxation times (T2*) were measured for each liquid in each bone powder. As bone density and surface to volume ratio increased, T1 decreased faster for saline than for oil. T2* decreased significantly for both water and oil as the surface to volume ratio increased. It was concluded that effects of water on T1 could be explained by a surface interaction at the bone/liquid interface, which restricted rotational and translational motion of nearby molecules. The T1s of oil were not affected since oil molecules are nonpolar, do not participate in significant intermolecular hydrogen bonding, and therefore would not be expected to interact strongly with the bone surface. Effects on T2* could be explained by local magnetic field inhomogeneities created by discontinuous magnetic susceptibility near the bone surface. These preliminary results suggest that water in contact with trabecular bone in vivo will exhibit shortened relaxation times.

  1. Characterization of pH titration shifts for all the nonlabile proton resonances a protein by two-dimensional NMR: the case of mouse epidermal growth factor.

    PubMed

    Kohda, D; Sawada, T; Inagaki, F

    1991-05-21

    The pH titration shifts for all the nonlabile proton resonances in a 53-residue protein (mouse epidermal growth factor) were measured in the p2H range 1.5-9 with two-dimensional (2D) 1H NMR. The 2D NMR pH titration experiment made it possible to determine the pK values for all the ionizable groups which were titrated in the pH range 1.5-9 in the protein. The pK values of the nine ionizable groups (alpha-amino group, four Asp, two Glu, one His, and alpha-carboxyl group) were found to be near their normal values. The 2D titration experiment also provided a detailed description of the pH-dependent behavior of the proton chemical shifts and enabled us to characterize the pH-dependent changes of protein conformation. Analysis of the pH-dependent shifts of ca. 200 proton resonances offered evidence of conformational changes in slightly basic pH solution: The deprotonation of the N-terminal alpha-amino group induced a widespread conformational change over the beta-sheet structure in the protein, while the effects of deprotonation of the His22 imidazole group were relatively localized. We found that the 2D NMR pH titration experiment is a powerful tool for investigating the structural and dynamic properties of proteins. PMID:2036358

  2. Characterization of pH titration shifts for all the nonlabile proton resonances in a protein by two-dimensional NMR: The case of mouse epidermal growth factor

    SciTech Connect

    Kohda, Daisuke; Sawada, Toshie; Inagaki, Fuyuhiko )

    1991-05-21

    The pH titration shifts for all the nonlabile proton resonances in a 53-residue protein (mouse epidermal growth factor) were measured in the p{sup 2}H range 1.5-9 with two-dimensional (2D) {sup 1}H NMR. The 2D NMR pH titration experiment made it possible to determine the pK values for all the ionizable group which were titrated in the pH range 1.5-9 in the protein. The pK values of the nine ionizable groups ({alpha}-amino group, four Asp, two Glu, one His, and {alpha}-carboxyl group) were found to be near their normal values. The 2D titration experiment also provided a detailed description of the pH-dependent behavior of the proton chemical shifts and enabled us to characterize the pH-dependent changes of protein conformation. Analysis of the pH-dependent shifts of ca. 200 proton resonances offered evidence of conformational changes in slightly basic pH solution: The deprotonation of the N-terminal {alpha}-amino group induced a widespread conformational change over the {beta}-sheet structure in the protein, while the effects of deprotonation of the His22 imidazole group were relatively localized. The authors found that the 2D NMR pH titration experiment is a powerful tool for investigating the structural and dynamic properties of proteins.

  3. Proton NMR analysis of octane number for motor gasoline: Part IV

    SciTech Connect

    Ichikawa, M.; Nonaka, N.; Amano, H.; Takada, I.; Ishimori, S.; Andoh, H.; Kumamoto, K.

    1992-08-01

    Software for predicting the octane number of motor gasoline by proton magnetic resonance (PMR) spectrometry has been formulated. At the same time, a method has been studied to predict the composition of gasoline (in terms of the contents of paraffin, olefin, and aromatic compounds). The formulated program was evaluated by using it to predict the octane numbers of 31 samples of marketed summer gasoline (including 16 regular and 15 premium products), whose octane numbers and compositions were identified according to the ASTM standards. Also, the relationship between the PMR spectrum and gasoline composition was subjected to linear regression analysis by using the 31 samples whose octane numbers were calculated, and the appropriateness of the resultant regression equations was assessed. This report concerns the results of the study in which the octane numbers of the 31 samples were satisfactorily predicted by the formulated program and useful linear regression equation were obtained for the prediction of the composition of gasoline. 9 refs., 9 figs., 3 tabs.

  4. The Peculiarities of the NMR Spin-Lattice Relaxation in Proton Exchanged LINBO_{3}

    NASA Astrophysics Data System (ADS)

    Vertegel, Igor; Chesnokov, Eugeny; Ovcharenko, Alexander; Vertegel, Ivan

    2013-06-01

    The temperature dependence of the spin-lattice relaxation time T_{1} of Li^{7} nuclei in the temperature range (170-430 K) was investigated in LiNbO_{3} polycrystalline samples: the clean and annealed ones in a hydrogen environment at temperature around 1000° C. The anomaly in the temperature dependence of T_{1} was found in range 300-340 K for both pure and annealed crystals. The reduction of the time T_{1} in the annealed lithium niobate crystal is caused by the creation of point defects (F^{+} or F-centers), with the dominant F-centers contribution. An increase in the activation energy in the annealed crystal can be explained by the following. It is known for the pure lithium niobate that an oscillation of lithium occurs in a symmetrical potential consisting of three wells. Formation of the oxygen vacancies in the annealed crystals is accompanied with extrinsic protons occupation of the vacancies. It leads to the symmetry violation and causes an i ncrease of the activation barrier.

  5. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I.

    PubMed

    Sazanov, Leonid A

    2014-08-01

    NADH-ubiquinone oxidoreductase (complex I) is the first and largest enzyme in the respiratory chain of mitochondria and many bacteria. It couples the transfer of two electrons between NADH and ubiquinone to the translocation of four protons across the membrane. Complex I is an L-shaped assembly formed by the hydrophilic (peripheral) arm, containing all the redox centres performing electron transfer and the membrane arm, containing proton-translocating machinery. Mitochondrial complex I consists of 44 subunits of about 1 MDa in total, whilst the prokaryotic enzyme is simpler and generally consists of 14 conserved "core" subunits. Recently we have determined the first atomic structure of the entire complex I, using the enzyme from Thermus thermophilus (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM helices). Structure suggests a unique coupling mechanism, with redox energy of electron transfer driving proton translocation via long-range (up to ~200 Å) conformational changes. It resembles a steam engine, with coupling elements (akin to coupling rods) linking parts of this molecular machine. PMID:24943718

  6. Surface Proton Hopping and Coupling Pathway of Water Oxidation on Cobalt Oxide Catalyst

    NASA Astrophysics Data System (ADS)

    Pham, Hieu; Cheng, Mu-Jeng; Frei, Heinz; Wang, Lin-Wang

    We propose an oxidation pathway of water splitting on cobalt oxide surface with clear thermodynamic and kinetic details. The density-functional theory studies suggest that the coupled proton-electron transfer is not necessarily sequential and implicit in every elementary step of this mechanistic cycle. Instead, the initial O-O bond could be formed by the landing of water molecule on the surface oxos, which is then followed by the dispatch of protons through the hopping manner and subsequent release of di-oxygen. Our theoretical investigations of intermediates and transition states indicate that all chemical conversions in this pathway, including the proton transfers, are possible with low activation barriers, in addition to their favorable thermodynamics. Our hypothesis is supported by recent experimental observations of surface superoxide that is stabilized by hydrogen bonding to adjacent hydroxyl group, as an intermediate on fast-kinetics catalytic site.

  7. A protonation-coupled feedback mechanism controls the signalling process in bathy phytochromes

    NASA Astrophysics Data System (ADS)

    Velazquez Escobar, Francisco; Piwowarski, Patrick; Salewski, Johannes; Michael, Norbert; Fernandez Lopez, Maria; Rupp, Anna; Muhammad Qureshi, Bilal; Scheerer, Patrick; Bartl, Franz; Frankenberg-Dinkel, Nicole; Siebert, Friedrich; Andrea Mroginski, Maria; Hildebrandt, Peter

    2015-05-01

    Phytochromes are bimodal photoswitches composed of a photosensor and an output module. Photoactivation of the sensor is initiated by a double bond isomerization of the tetrapyrrole chromophore and eventually leads to protein conformational changes. Recently determined structural models of phytochromes identify differences between the inactive and the signalling state but do not reveal the mechanism of photosensor activation or deactivation. Here, we report a vibrational spectroscopic study on bathy phytochromes that demonstrates that the formation of the photoactivated state and thus (de)activation of the output module is based on proton translocations in the chromophore pocket coupling chromophore and protein structural changes. These proton transfer steps, involving the tetrapyrrole and a nearby histidine, also enable thermal back-isomerization of the chromophore via keto-enol tautomerization to afford the initial dark state. Thus, the same proton re-arrangements inducing the (de)activation of the output module simultaneously initiate the reversal of this process, corresponding to a negative feedback mechanism.

  8. Novel macrocyclic carriers for proton-coupled liquid membrane transport. Progress report, 1 December 1988--31 May 1991

    SciTech Connect

    Lamb, J.D.

    1991-06-10

    The objective of our research program is to elucidate the chemical principles which are responsible for the cation selectivity and permeability of liquid membranes containing macrocyclic carriers. Several new macrocyclic carriers were synthesized during the last three year period, including selenium-containing macrocycles, new crown-4 structures, and several new crown structures containing nitrogen based heterocycles as substituents in the principal macrocyclic ring. The cation binding properties of these macrocycles were investigated by potentiometric titration, calorimetric titration, solvent extraction, and NMR techniques. In addition, hydrophobic macrocycles were incorporated into dual hollow fiber membrane systems to investigate their membrane performance, especially in the proton-coupled transport mode. It was found that the dual hollow fiber system maintains the cation selectivity and permeability of supported liquid membranes, while enhancing membrane stability. The diffusion limited transport model was expanded to account for membrane solvent effects. Furthermore, Eu{sup 2+} transport was found to be similar to that of strontium and much higher than that of the lanthanides, in supported liquid membrane systems.

  9. Photochemical Tyrosine Oxidation with a Hydrogen-Bonded Proton Acceptor by Bidirectional Proton-Coupled Electron Transfer

    PubMed Central

    Pizano, Arturo A.; Yang, Jay L.

    2012-01-01

    Amino acid radical generation and transport are fundamentally important to numerous essential biological processes to which small molecule models lend valuable mechanistic insights. Pyridyl-amino acid-methyl esters are appended to a rhenium(I) tricarbonyl 1,10-phenanthroline core to yield rhenium–amino acid complexes with tyrosine ([Re]–Y–OH) and phenylalanine ([Re]–F). The emission from the [Re] center is more significantly quenched for [Re]–Y–OH upon addition of base. Time-resolved studies establish that excited-state quenching occurs by a combination of static and dynamic mechanisms. The degree of quenching depends on the strength of the base, consistent with a proton-coupled electron transfer (PCET) quenching mechanism. Comparative studies of [Re]–Y–OH and [Re]–F enable a detailed mechanistic analysis of a bidirectional PCET process. PMID:23495362

  10. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II.

    PubMed

    Taraphder, Srabani; Maupin, C Mark; Swanson, Jessica M J; Voth, Gregory A

    2016-08-25

    The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II. Special attention has been placed on whether the motion of an excess proton is correlated with fluctuations in the surrounding protein and solvent matrix, which may be rare on the picosecond and subpicosecond time scales of molecular motions. It is found that several active site residues, which do not directly participate in the proton transport event, have a significant impact on the dynamics of the excess proton. These secondary participants are shown to strongly influence the active site environment, resulting in the creation of water clusters that are conducive to fast, moderately slow, or slow proton transport events. The identification and characterization of these secondary participants illuminates the role of protein dynamics in the catalytic efficiency of HCA II. PMID:27063577

  11. Mixed Quantum-Classical Liouville Approach for Calculating Proton-Coupled Electron-Transfer Rate Constants.

    PubMed

    Shakib, Farnaz; Hanna, Gabriel

    2016-07-12

    In this work, we derive a general mixed quantum-classical formula for calculating thermal proton-coupled electron-transfer (PCET) rate constants, starting from the time integral of the quantum flux-flux correlation function. This formula allows for the direct simulation of PCET reaction dynamics via the mixed quantum-classical Liouville approach. Owing to the general nature of the derivation, this formula does not rely on any prior mechanistic assumptions and can be applied across a wide range of electronic and protonic coupling regimes. To test the validity of this formula, we applied it to a reduced model of a condensed-phase PCET reaction. Good agreement with the numerically exact rate constant is obtained, demonstrating the accuracy of our formalism. We believe that this approach constitutes a solid foundation for future investigations of the rates and mechanisms of a wide range of PCET reactions. PMID:27232936

  12. Molecular structure, tautomeric stability, protonation and deprotonation effects, vibrational, NMR and NBO analyses of 2,4-Dioxoimidazolidine-5-acetic acid (DOIAA) by quantum chemical calculations.

    PubMed

    Sridevi, C; Velraj, G

    2014-01-01

    This study represents the conformation, tautomeric stability, protonation and deprotonation effects, vibrational, electronic, NBO and NMR aspects of 2,4-Dioxoimidazolidine-5-acetic acid (DOIAA). Theoretical calculations were performed by ab initio HF and density functional theory (DFT)/B3LYP method using 6-311++G(d,p) basis sets. Tautomerism and the effect of solvent on the tautomeric equilibria in the gas phase and in different solvents were studied. The protonation and deprotonation effects on the reactivity and conformations of DOIAA were investigated. Electronic transitions were also studied and the most prominent transition corresponds to π→π*. Natural bond orbital (NBO) analysis was also carried out to find the intramolecular interactions and their stabilization energy. In DOIAA, the interaction between the lone pair donor orbital (n(LP1N5)) and the acceptor antibonding orbital π*(C6O7) reveals the strong stabilization energy of 224.9 kJ mol(-1). Molecular electrostatic potential (MEP) was calculated to predict the reactive sites of the title compound. The NMR results indicated that the observed chemical shifts for NH, COOH protons of DOIAA not only depend on the structure of the molecule being studied but also on the nature of the solvent, concentration of the sample and the presence of the other exchangeable protons. PMID:24291430

  13. Composite-180° pulse-based symmetry sequences to recouple proton chemical shift anisotropy tensors under ultrafast MAS solid-state NMR spectroscopy.

    PubMed

    Pandey, Manoj Kumar; Malon, Michal; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

    2015-01-01

    There is considerable interest in the measurement of proton ((1)H) chemical shift anisotropy (CSA) tensors to obtain deeper insights into H-bonding interactions which find numerous applications in chemical and biological systems. However, the presence of strong (1)H/(1)H dipolar interaction makes it difficult to determine small size (1)H CSAs from the homogeneously broadened NMR spectra. Previously reported pulse sequences for (1)H CSA recoupling are prone to the effects of radio frequency field (B1) inhomogeneity. In the present work we have carried out a systematic study using both numerical and experimental approaches to evaluate γ-encoded radio frequency (RF) pulse sequences based on R-symmetries that recouple (1)H CSA in the indirect dimension of a 2D (1)H/(1)H anisotropic/isotropic chemical shift correlation experiment under ultrafast magic angle spinning (MAS) frequencies. The spectral resolution and sensitivity can be significantly improved in both frequency dimensions of the 2D (1)H/(1)H correlation spectrum without decoupling (1)H/(1)H dipolar couplings but by using ultrafast MAS rates up to 70 kHz. We successfully demonstrate that with a reasonable RF field requirement (<200 kHz) a set of symmetry-based recoupling sequences, with a series of phase-alternating 270°0-90°180 composite-180° pulses, are more robust in combating B1 inhomogeneity effects. In addition, our results show that the new pulse sequences render remarkable (1)H CSA recoupling efficiency and undistorted CSA lineshapes. Experimental results on citric acid and malonic acid comparing the efficiencies of these newly developed pulse sequences with that of previously reported CSA recoupling pulse sequences are also reported under ultrafast MAS conditions. PMID:25497846

  14. Differentiation of enantiomers by 2D NMR spectroscopy at 1 T using residual dipolar couplings.

    PubMed

    Koos, Martin R M; Danieli, Ernesto; Casanova, Federico; Blümich, Bernhard; Luy, Burkhard

    2016-06-01

    Differentiating enantiomers using 2D bench-top NMR spectroscopy. Spectrometers working with permanent magnets at 1 T field strength allow the acquisition of 2D data sets. In conjunction with previously reported chiral alignment media, this setup allows the measurement of enantiomeric excess via residual dipolar couplings in stretched gelatine as a result of the reduced line width obtained by 2D J-resolved spectroscopy. PMID:25773020

  15. ATP-dependent substrate transport by the ABC transporter MsbA is proton-coupled.

    PubMed

    Singh, Himansha; Velamakanni, Saroj; Deery, Michael J; Howard, Julie; Wei, Shen L; van Veen, Hendrik W

    2016-01-01

    ATP-binding cassette transporters mediate the transbilayer movement of a vast number of substrates in or out of cells in organisms ranging from bacteria to humans. Current alternating access models for ABC exporters including the multidrug and Lipid A transporter MsbA from Escherichia coli suggest a role for nucleotide as the fundamental source of free energy. These models involve cycling between conformations with inward- and outward-facing substrate-binding sites in response to engagement and hydrolysis of ATP at the nucleotide-binding domains. Here we report that MsbA also utilizes another major energy currency in the cell by coupling substrate transport to a transmembrane electrochemical proton gradient. The dependence of ATP-dependent transport on proton coupling, and the stimulation of MsbA-ATPase by the chemical proton gradient highlight the functional integration of both forms of metabolic energy. These findings introduce ion coupling as a new parameter in the mechanism of this homodimeric ABC transporter. PMID:27499013

  16. ATP-dependent substrate transport by the ABC transporter MsbA is proton-coupled

    PubMed Central

    Singh, Himansha; Velamakanni, Saroj; Deery, Michael J.; Howard, Julie; Wei, Shen L.; van Veen, Hendrik W.

    2016-01-01

    ATP-binding cassette transporters mediate the transbilayer movement of a vast number of substrates in or out of cells in organisms ranging from bacteria to humans. Current alternating access models for ABC exporters including the multidrug and Lipid A transporter MsbA from Escherichia coli suggest a role for nucleotide as the fundamental source of free energy. These models involve cycling between conformations with inward- and outward-facing substrate-binding sites in response to engagement and hydrolysis of ATP at the nucleotide-binding domains. Here we report that MsbA also utilizes another major energy currency in the cell by coupling substrate transport to a transmembrane electrochemical proton gradient. The dependence of ATP-dependent transport on proton coupling, and the stimulation of MsbA-ATPase by the chemical proton gradient highlight the functional integration of both forms of metabolic energy. These findings introduce ion coupling as a new parameter in the mechanism of this homodimeric ABC transporter. PMID:27499013

  17. Analysis of kinetic isotope effects for proton-coupled electron transfer reactions.

    PubMed

    Edwards, Sarah J; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2009-03-12

    A series of rate constant expressions for nonadiabatic proton-coupled electron transfer (PCET) reactions are analyzed and compared. The approximations underlying each expression are enumerated, and the regimes of validity for each expression are illustrated by calculations on model systems. In addition, the kinetic isotope effects (KIEs) for a series of model PCET reactions are analyzed to elucidate the fundamental physical principles dictating the magnitude of the KIE and the dependence of the KIE on the physical properties of the system, including temperature, reorganization energy, driving force, equilibrium proton donor-acceptor distance, and effective frequency of the proton donor-acceptor mode. These calculations lead to three physical insights that are directly relevant to experimental data. First, these calculations provide an explanation for a decrease in the KIE as the proton donor-acceptor distance increases, even though typically the KIE will increase with increasing equilibrium proton donor-acceptor distance if all other parameters remain fixed. Often the proton donor-acceptor frequency decreases as the proton donor-acceptor distance increases, and these two effects impact the KIE in opposite directions, so either trend could be observed. Second, these calculations provide an explanation for an increase in the KIE as the temperature increases, even though typically the KIE will decrease with increasing temperature if all other parameters remain fixed. The combination of a rigid hydrogen bond, which corresponds to a high proton donor-acceptor frequency, and low solvent polarity, which corresponds to small solvent reorganization energy, allows the KIE to either increase or decrease with temperature, depending on the other properties of the system. Third, these calculations provide insight into the dependence of the rate constant and KIE on the driving force, which has been studied experimentally for a wide range of PCET systems. The rate constant

  18. Compositional differences among Chinese soy sauce types studied by (13)C NMR spectroscopy coupled with multivariate statistical analysis.

    PubMed

    Kamal, Ghulam Mustafa; Wang, Xiaohua; Bin Yuan; Wang, Jie; Sun, Peng; Zhang, Xu; Liu, Maili

    2016-09-01

    Soy sauce a well known seasoning all over the world, especially in Asia, is available in global market in a wide range of types based on its purpose and the processing methods. Its composition varies with respect to the fermentation processes and addition of additives, preservatives and flavor enhancers. A comprehensive (1)H NMR based study regarding the metabonomic variations of soy sauce to differentiate among different types of soy sauce available on the global market has been limited due to the complexity of the mixture. In present study, (13)C NMR spectroscopy coupled with multivariate statistical data analysis like principle component analysis (PCA), and orthogonal partial least square-discriminant analysis (OPLS-DA) was applied to investigate metabonomic variations among different types of soy sauce, namely super light, super dark, red cooking and mushroom soy sauce. The main additives in soy sauce like glutamate, sucrose and glucose were easily distinguished and quantified using (13)C NMR spectroscopy which were otherwise difficult to be assigned and quantified due to serious signal overlaps in (1)H NMR spectra. The significantly higher concentration of sucrose in dark, red cooking and mushroom flavored soy sauce can directly be linked to the addition of caramel in soy sauce. Similarly, significantly higher level of glutamate in super light as compared to super dark and mushroom flavored soy sauce may come from the addition of monosodium glutamate. The study highlights the potentiality of (13)C NMR based metabonomics coupled with multivariate statistical data analysis in differentiating between the types of soy sauce on the basis of level of additives, raw materials and fermentation procedures. PMID:27343582

  19. Dipolar-coupling-mediated total correlation spectroscopy in solid-state 13C NMR: Selection of individual 13C- 13C dipolar interactions

    NASA Astrophysics Data System (ADS)

    Spano, Justin; Wi, Sungsool

    2010-06-01

    Herein is described a useful approach in solid-state NMR, for selecting homonuclear 13C- 13C spin pairs in a multiple- 13C homonuclear dipolar coupled spin system. This method builds upon the zero-quantum (ZQ) dipolar recoupling method introduced by Levitt and coworkers (Marin-Montesinos et al., 2006 [30]) by extending the originally introduced one-dimensional (1D) experiment into a two-dimensional (2D) method with selective irradiation scheme, while moving the 13C- 13C mixing scheme from the transverse to the longitudinal mode, together with a dramatic improvement in the proton decoupling efficiency. Selective spin-pair recoupling experiments incorporating Gaussian and cosine-modulated Gaussian pulses for inverting specific spins were performed, demonstrating the ability to detect informative, simplified/individualized, long-range 13C- 13C homonuclear dipolar coupling interactions more accurately by removing less informative, stronger, short-range 13C- 13C interactions from 2D correlation spectra. The capability of this new approach was demonstrated experimentally on uniformly 13C-labeled Glutamine and a tripeptide sample, GAL.

  20. The Use of Residual Dipolar Coupling in Studying Proteins by NMR

    PubMed Central

    Chen, Kang

    2014-01-01

    The development of residual dipolar coupling (RDC) in protein NMR spectroscopy, over a decade ago, has become a useful and almost routine tool for accurate protein solution structure determination. RDCs provide orientation information of magnetic dipole–dipole interaction vectors within a common reference frame. Its measurement requires a nonisotropic orientation, through a direct or indirect magnetic field alignment, of the protein in solution. There has been recent progress in the developments of alignment methods to allow the measurement of RDC and of methods to analyze the resulting data. In this chapter we briefly go through the mathematical expressions for the RDC and common descriptions of the alignment tensor, which may be represented using either Saupe order or the principal order matrix. Then we review the latest developments in alignment media. In particular we looked at the lipid-compatible media that allow the measurement of RDCs for membrane proteins. Other methods including conservative surface residue mutation have been invented to obtain up to five orthogonal alignment tensors that provide a potential for de novo structure and dynamics study using RDCs exclusively. We then discuss approximations assumed in RDC interpretations and different views on dynamics uncovered from the RDC method. In addition to routine usage of RDCs in refining a single structure, novel applications such as ensemble refinement against RDCs have been implemented to represent protein structure and dynamics in solution. The RDC application also extends to the study of protein–substrate interaction as well as to solving quaternary structure of oligomer in equilibrium with a monomer, opening an avenue for RDCs in high-order protein structure determination. PMID:21952837

  1. Basic principles of static proton low-resolution spin diffusion NMR in nanophase-separated materials with mobility contrast.

    PubMed

    Schäler, Kerstin; Roos, Matthias; Micke, Peter; Golitsyn, Yury; Seidlitz, Anne; Thurn-Albrecht, Thomas; Schneider, Horst; Hempel, Günter; Saalwächter, Kay

    2015-11-01

    We review basic principles of low-resolution proton NMR spin diffusion experiments, relying on mobility differences in nm-sized phases of inhomogeneous organic materials such as block-co- or semicrystalline polymers. They are of use for estimates of domain sizes and insights into nanometric dynamic inhomogeneities. Experimental procedures and limitations of mobility-based signal decomposition/filtering prior to spin diffusion are addressed on the example of as yet unpublished data on semicrystalline poly(ϵ-caprolactone), PCL. Specifically, we discuss technical aspects of the quantitative, dead-time free detection of rigid-domain signals by aid of the magic-sandwich echo (MSE), and magic-and-polarization-echo (MAPE) and double-quantum (DQ) magnetization filters to select rigid and mobile components, respectively. Such filters are of general use in reliable fitting approaches for phase composition determinations. Spin diffusion studies at low field using benchtop instruments are challenged by rather short (1)H T1 relaxation times, which calls for simulation-based analyses. Applying these, in combination with domain sizes as determined by small-angle X-ray scattering, we have determined spin diffusion coefficients D for PCL (0.34, 0.19 and 0.032nm(2)/ms for crystalline, interphase and amorphous parts, respectively). We further address thermal-history effects related to secondary crystallization. Finally, the state of knowledge concerning the connection between D values determined locally at the atomic level, using (13)C detection and CP- or REDOR-based "(1)H hole burning" procedures, and those obtained by calibration experiments, is summarized. Specifically, the non-trivial dependence of D on the magic-angle spinning (MAS) frequency, with a minimum under static and a local maximum under moderate-MAS conditions, is highlighted. PMID:26404771

  2. Effect of magnetic field and iron content on NMR proton relaxation of liver, spleen and brain tissues.

    PubMed

    Hocq, Aline; Luhmer, Michel; Saussez, Sven; Louryan, Stéphane; Gillis, Pierre; Gossuin, Yves

    2015-01-01

    Iron accumulation is observed in liver and spleen during hemochromatosis and important neurodegenerative diseases involve iron overload in brain. Storage of iron is ensured by ferritin, which contains a magnetic core. It causes a darkening on T2 -weighted MR images. This work aims at improving the understanding of the NMR relaxation of iron-loaded human tissues, which is necessary to develop protocols of iron content measurements by MRI. Relaxation times measurements on brain, liver and spleen samples were realized at different magnetic fields. Iron content was determined by atomic emission spectroscopy. For all samples, the longitudinal relaxation rate (1/T1 ) of tissue protons decreases with the magnetic field up to 1 T, independently of iron content, while their transverse relaxation rate (1/T2 ) strongly increases with the field, either linearly or quadratically, or a combination thereof. The extent of the inter-echo time dependence of 1/T2 also varies according to the sample. A combination of theoretical models is necessary to describe the relaxation of iron-containing tissues. This can be due to the presence, inside tissues, of ferritin clusters of different sizes and densities. When considering all samples, a correlation (r(2)  = 0.6) between 1/T1 and iron concentration is observed at 7.0 T. In contrast the correlation between 1/T2 and iron content is poor, even at high field (r(2)  = 0.14 at 7.0 T). Our results show that MRI methods based on T1 or T2 measurements will easily detect an iron overloading at high magnetic field, but will not provide an accurate quantification of tissue iron content at low iron concentrations. PMID:24954138

  3. Characterization of the Dynamics in the Protonic Conductor CsH2PO4 by 17O Solid-State NMR Spectroscopy and First-Principles Calculations: Correlating Phosphate and Protonic Motion

    PubMed Central

    2015-01-01

    17O NMR spectroscopy combined with first-principles calculations was employed to understand the local structure and dynamics of the phosphate ions and protons in the paraelectric phase of the proton conductor CsH2PO4. For the room-temperature structure, the results confirm that one proton (H1) is localized in an asymmetric H-bond (between O1 donor and O2 acceptor oxygen atoms), whereas the H2 proton undergoes rapid exchange between two sites in a hydrogen bond with a symmetric double potential well at a rate ≥107 Hz. Variable-temperature 17O NMR spectra recorded from 22 to 214 °C were interpreted by considering different models for the rotation of the phosphate anions. At least two distinct rate constants for rotations about four pseudo C3 axes of the phosphate ion were required in order to achieve good agreement with the experimental data. An activation energy of 0.21 ± 0.06 eV was observed for rotation about the P–O1 axis, with a higher activation energy of 0.50 ± 0.07 eV being obtained for rotation about the P–O2, P–O3d, and P–O3a axes, with the superscripts denoting, respectively, dynamic donor and acceptor oxygen atoms of the H-bond. The higher activation energy of the second process is most likely associated with the cost of breaking an O1–H1 bond. The activation energy of this process is slightly lower than that obtained from the 1H exchange process (0.70 ± 0.07 eV) (Kim, G.; Blanc, F.; Hu, Y.-Y.; Grey, C. P. J. Phys. Chem. C2013, 117, 6504−6515) associated with the translational motion of the protons. The relationship between proton jumps and phosphate rotation was analyzed in detail by considering uncorrelated motion, motion of individual PO4 ions and the four connected/H-bonded protons, and concerted motions of adjacent phosphate units, mediated by proton hops. We conclude that, while phosphate rotations aid proton motion, not all phosphate rotations result in proton jumps. PMID:25732257

  4. Accurate measurement of heteronuclear dipolar couplings by phase-alternating R-symmetry (PARS) sequences in magic angle spinning NMR spectroscopy

    SciTech Connect

    Hou, Guangjin E-mail: tpolenov@udel.edu; Lu, Xingyu E-mail: lexvega@comcast.net; Vega, Alexander J. E-mail: lexvega@comcast.net; Polenova, Tatyana E-mail: tpolenov@udel.edu

    2014-09-14

    We report a Phase-Alternating R-Symmetry (PARS) dipolar recoupling scheme for accurate measurement of heteronuclear {sup 1}H-X (X = {sup 13}C, {sup 15}N, {sup 31}P, etc.) dipolar couplings in MAS NMR experiments. It is an improvement of conventional C- and R-symmetry type DIPSHIFT experiments where, in addition to the dipolar interaction, the {sup 1}H CSA interaction persists and thereby introduces considerable errors in the dipolar measurements. In PARS, phase-shifted RN symmetry pulse blocks applied on the {sup 1}H spins combined with π pulses applied on the X spins at the end of each RN block efficiently suppress the effect from {sup 1}H chemical shift anisotropy, while keeping the {sup 1}H-X dipolar couplings intact. Another advantage over conventional DIPSHIFT experiments, which require the signal to be detected in the form of a reduced-intensity Hahn echo, is that the series of π pulses refocuses the X chemical shift and avoids the necessity of echo formation. PARS permits determination of accurate dipolar couplings in a single experiment; it is suitable for a wide range of MAS conditions including both slow and fast MAS frequencies; and it assures dipolar truncation from the remote protons. The performance of PARS is tested on two model systems, [{sup 15}N]-N-acetyl-valine and [U-{sup 13}C,{sup 15}N]-N-formyl-Met-Leu-Phe tripeptide. The application of PARS for site-resolved measurement of accurate {sup 1}H-{sup 15}N dipolar couplings in the context of 3D experiments is presented on U-{sup 13}C,{sup 15}N-enriched dynein light chain protein LC8.

  5. Accurate measurement of heteronuclear dipolar couplings by phase-alternating R-symmetry (PARS) sequences in magic angle spinning NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Hou, Guangjin; Lu, Xingyu; Vega, Alexander J.; Polenova, Tatyana

    2014-09-01

    We report a Phase-Alternating R-Symmetry (PARS) dipolar recoupling scheme for accurate measurement of heteronuclear 1H-X (X = 13C, 15N, 31P, etc.) dipolar couplings in MAS NMR experiments. It is an improvement of conventional C- and R-symmetry type DIPSHIFT experiments where, in addition to the dipolar interaction, the 1H CSA interaction persists and thereby introduces considerable errors in the dipolar measurements. In PARS, phase-shifted RN symmetry pulse blocks applied on the 1H spins combined with π pulses applied on the X spins at the end of each RN block efficiently suppress the effect from 1H chemical shift anisotropy, while keeping the 1H-X dipolar couplings intact. Another advantage over conventional DIPSHIFT experiments, which require the signal to be detected in the form of a reduced-intensity Hahn echo, is that the series of π pulses refocuses the X chemical shift and avoids the necessity of echo formation. PARS permits determination of accurate dipolar couplings in a single experiment; it is suitable for a wide range of MAS conditions including both slow and fast MAS frequencies; and it assures dipolar truncation from the remote protons. The performance of PARS is tested on two model systems, [15N]-N-acetyl-valine and [U-13C,15N]-N-formyl-Met-Leu-Phe tripeptide. The application of PARS for site-resolved measurement of accurate 1H-15N dipolar couplings in the context of 3D experiments is presented on U-13C,15N-enriched dynein light chain protein LC8.

  6. A capacitively coupled temperature-jump arrangement for high-resolution biomolecular NMR.

    PubMed

    Gal, Maayan; Zibzener, Koby; Frydman, Lucio

    2010-11-01

    A simple design for performing rapid temperature jumps within a high-resolution nuclear magnetic resonance (NMR) setting is presented and exemplified. The design is based on mounting, around a conventional NMR glass tube, an inductive radiofrequency (RF) irradiation coil that is suitably tuned by a resonant circuit and is driven by one of the NMR's console high-power RF amplifiers. The electric fields generated by this coil's thin metal strips can lead to a fast and efficient heating of the sample, amounting to temperature jumps of ≈ 20 °C in well within a second-particularly in the presence of lossy dielectric media like those provided by physiological buffers. Moreover, when wound around a 4-mm NMR tube, the resulting device fits a conventional 5-mm inverse probe and is wholly compatible with the field homogeneities and sensitivities expected for high-resolution biomolecular NMR conditions. The performance characteristics of this new system were tested using saline solutions, as well as on a lyotropic liquid crystal capable of undergoing nematic → isotropic transitions in the neighborhood of ambient temperature. These settings were then incorporated into the performance of a new kind of single-scan 2D NMR spectroscopy acquisition, correlating the anisotropic and isotropic patterns elicited by solutes dissolved in such liquid-crystalline systems, before and after a sudden temperature jump occurring during an intervening mixing period. PMID:20818777

  7. Proton Quantization and Vibrational Relaxation in Nonadiabatic Dynamics of Photoinduced Proton-Coupled Electron Transfer in a Solvated Phenol-Amine Complex.

    PubMed

    Goyal, Puja; Schwerdtfeger, Christine A; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2016-03-10

    Nonadiabatic dynamics simulations of photoinduced proton-coupled electron transfer (PCET) in a phenol-amine complex in solution were performed. The electronic potential energy surfaces were generated on-the-fly with a hybrid quantum mechanical/molecular mechanical approach that described the solute with a multiconfigurational method in a bath of explicit solvent molecules. The transferring hydrogen nucleus was represented as a quantum mechanical wave function calculated with grid-based methods, and surface hopping trajectories were propagated on the adiabatic electron-proton vibronic surfaces. Following photoexcitation to the excited S1 electronic state, the overall decay to the ground vibronic state was found to be comprised of relatively fast decay from a lower proton vibrational state of S1 to a highly excited proton vibrational state of the ground S0 electronic state, followed by vibrational relaxation within the S0 state. Proton transfer can occur either on the highly excited proton vibrational states of S0 due to small environmental fluctuations that shift the delocalized vibrational wave functions or on the low-energy proton vibrational states of S1 due to solvent reorganization that alters the asymmetry of the proton potential and reduces the proton transfer barrier. The isotope effect arising from replacing the transferring hydrogen with deuterium is predicted to be negligible because hydrogen and deuterium behave similarly in both types of proton transfer processes. Although an isotope effect could be observed for other systems, in general the absence of an isotope effect does not imply the absence of proton transfer in photoinduced PCET systems. This computational approach is applicable to a wide range of other photoinduced PCET processes. PMID:26812149

  8. The possible role of proton-coupled electron transfer (PCET) in water oxidation by photosystem II.

    PubMed

    Meyer, Thomas J; Huynh, My Hang V; Thorp, H Holden

    2007-01-01

    All higher life forms use oxygen and respiration as their primary energy source. The oxygen comes from water by solar-energy conversion in photosynthetic membranes. In green plants, light absorption in photosystem II (PSII) drives electron-transfer activation of the oxygen-evolving complex (OEC). The mechanism of water oxidation by the OEC has long been a subject of great interest to biologists and chemists. With the availability of new molecular-level protein structures from X-ray crystallography and EXAFS, as well as the accumulated results from numerous experiments and theoretical studies, it is possible to suggest how water may be oxidized at the OEC. An integrated sequence of light-driven reactions that exploit coupled electron-proton transfer (EPT) could be the key to water oxidation. When these reactions are combined with long-range proton transfer (by sequential local proton transfers), it may be possible to view the OEC as an intricate structure that is "wired for protons". PMID:17604381

  9. G2A is a proton-sensing G-protein-coupled receptor antagonized by lysophosphatidylcholine.

    PubMed

    Murakami, Naoka; Yokomizo, Takehiko; Okuno, Toshiaki; Shimizu, Takao

    2004-10-01

    G2A (from G2 accumulation) is a G-protein-coupled receptor (GPCR) that regulates the cell cycle, proliferation, oncogenesis, and immunity. G2A shares significant homology with three GPCRs including ovarian cancer GPCR (OGR1/GPR68), GPR4, and T cell death-associated gene 8 (TDAG8). Lysophosphatidylcholine (LPC) and sphingosylphosphorylcholine (SPC) were reported as ligands for G2A and GPR4 and for OGR1 (SPC only), and a glycosphingolipid psychosine was reported as ligand for TDAG8. As OGR1 and GPR4 were reported as proton-sensing GPCRs (Ludwig, M. G., Vanek, M., Guerini, D., Gasser, J. A., Jones, C. E., Junker, U., Hofstetter, H., Wolf, R. M., and Seuwen, K. (2003) Nature 425, 93-98), we evaluated the proton-sensing function of G2A. Transient expression of G2A caused significant activation of the zif 268 promoter and inositol phosphate (IP) accumulation at pH 7.6, and lowering extracellular pH augmented the activation only in G2A-expressing cells. LPC inhibited the pH-dependent activation of G2A in a dose-dependent manner in these assays. Thus, G2A is another proton-sensing GPCR, and LPC functions as an antagonist, not as an agonist, and regulates the proton-dependent activation of G2A. PMID:15280385

  10. Proton coupled electron transfer from the excited state of a ruthenium(II) pyridylimidazole complex.

    PubMed

    Pannwitz, Andrea; Wenger, Oliver S

    2016-04-28

    Proton coupled electron transfer (PCET) from the excited state of [Ru(bpy)2pyimH](2+) (bpy = 2,2'-bipyridine; pyimH = 2-(2'-pyridyl)imidazole) to N-methyl-4,4'-bipyridinium (monoquat, MQ(+)) was studied. While this complex has been investigated previously, our study is the first to show that the formal bond dissociation free energy (BDFE) of the imidazole-N-H bond decreases from (91 ± 1) kcal mol(-1) in the electronic ground state to (43 ± 5) kcal mol(-1) in the lowest-energetic (3)MLCT excited state. This makes the [Ru(bpy)2pyimH](2+) complex a very strong (formal) hydrogen atom donor even when compared to metal hydride complexes, and this is interesting for light-driven (formal) hydrogen atom transfer (HAT) reactions with a variety of different substrates. Mechanistically, formal HAT between (3)MLCT excited [Ru(bpy)2pyimH](2+) and monoquat in buffered 1 : 1 (v : v) CH3CN/H2O was found to occur via a sequence of reaction steps involving electron transfer from Ru(ii) to MQ(+) coupled to release of the N-H proton to buffer base, followed by protonation of reduced MQ(+) by buffer acid. Our study is relevant in the larger contexts of photoredox catalysis and light-to-chemical energy conversion. PMID:27094541